library(readr)
library(ggplot2)
library(lattice)
library(ggridges)
library(ggvis)
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## resolution
library(ggthemes)
library(cowplot)
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## Attaching package: 'cowplot'
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##
## theme_map
library(gapminder)
library(gganimate)
## No renderer backend detected. gganimate will default to writing frames to separate files
## Consider installing:
## - the `gifski` package for gif output
## - the `av` package for video output
## and restarting the R session
##
## Attaching package: 'gganimate'
## The following object is masked from 'package:ggvis':
##
## view_static
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(tidyverse)
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2
## ──
## ✔ tibble 3.1.8 ✔ stringr 1.5.0
## ✔ tidyr 1.3.0 ✔ forcats 1.0.0
## ✔ purrr 1.0.1
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library(grid)
library(gridExtra)
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## combine
library(RColorBrewer)
library(readr)
#Covid-liver cancer Example
Cancer<- read_csv("~/Downloads/Breast_Cancer.csv")
## Rows: 379 Columns: 7
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): Survivor, Stage
## dbl (5): Age, Tumor Size, Regional Node Examined, Reginol Node Positive, Sur...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Cancer
## # A tibble: 379 × 7
## Survivor Age Stage `Tumor Size` `Regional Node Examined` Reginol …¹ Survi…²
## <chr> <dbl> <chr> <dbl> <dbl> <dbl> <dbl>
## 1 Alive 68 T1 4 24 1 60
## 2 Alive 50 T2 35 14 5 62
## 3 Alive 58 T3 63 14 7 75
## 4 Alive 58 T1 18 2 1 84
## 5 Alive 47 T2 41 3 1 50
## 6 Alive 51 T1 20 18 2 89
## 7 Alive 51 T1 8 11 1 54
## 8 Dead 40 T2 30 9 1 14
## 9 Alive 40 T4 103 20 18 70
## 10 Alive 69 T4 32 21 12 92
## # … with 369 more rows, and abbreviated variable names
## # ¹​`Reginol Node Positive`, ²​`Survival Months`
str(Cancer)
## spc_tbl_ [379 × 7] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
## $ Survivor : chr [1:379] "Alive" "Alive" "Alive" "Alive" ...
## $ Age : num [1:379] 68 50 58 58 47 51 51 40 40 69 ...
## $ Stage : chr [1:379] "T1" "T2" "T3" "T1" ...
## $ Tumor Size : num [1:379] 4 35 63 18 41 20 8 30 103 32 ...
## $ Regional Node Examined: num [1:379] 24 14 14 2 3 18 11 9 20 21 ...
## $ Reginol Node Positive : num [1:379] 1 5 7 1 1 2 1 1 18 12 ...
## $ Survival Months : num [1:379] 60 62 75 84 50 89 54 14 70 92 ...
## - attr(*, "spec")=
## .. cols(
## .. Survivor = col_character(),
## .. Age = col_double(),
## .. Stage = col_character(),
## .. `Tumor Size` = col_double(),
## .. `Regional Node Examined` = col_double(),
## .. `Reginol Node Positive` = col_double(),
## .. `Survival Months` = col_double()
## .. )
## - attr(*, "problems")=<externalptr>
#Get the Correlations between the measurements
Cancer$Stage<-as.numeric(factor(Cancer$Stage, labels=c("1","2","3","4")))
Cancer1=cor(Cancer[-1])
colMeans(Cancer1)
## Age Stage Tumor Size
## 0.08831564 0.32741868 0.32781241
## Regional Node Examined Reginol Node Positive Survival Months
## 0.25464267 0.31035610 0.10189760
library (ggplot2)
ggplot(Cancer, aes(x=Stage, fill=Survivor))+geom_boxplot()+ labs(title='Survivorship comparison')
ggplot(Cancer, aes(x=Survivor,y=Stage)) + geom_boxplot()
# Using prcomp to compute the principal components (eigenvalues and eigenvectors). With scale=TRUE, variable means are set to zero, and variances set to one
Cancer_pca <- prcomp(Cancer[,-1],scale=TRUE)
Cancer_pca
## Standard deviations (1, .., p=6):
## [1] 1.4959541 1.0793515 0.9891605 0.9596806 0.7141874 0.4331658
##
## Rotation (n x k) = (6 x 6):
## PC1 PC2 PC3 PC4
## Age -0.2153849 0.21608166 -0.34917081 -0.88535662
## Stage 0.5628689 -0.32693628 0.06177527 -0.24457235
## Tumor Size 0.5822135 -0.28223117 -0.01433325 -0.21375444
## Regional Node Examined 0.2375181 0.75305159 0.21117279 0.02093686
## Reginol Node Positive 0.4590407 0.43924020 0.01680220 0.01827332
## Survival Months -0.1751633 -0.08214803 0.91059423 -0.33145859
## PC5 PC6
## Age -0.03346239 0.004663803
## Stage 0.18847337 0.690751203
## Tumor Size 0.13490974 -0.719218983
## Regional Node Examined 0.57570300 -0.005676451
## Reginol Node Positive -0.77028208 0.048979548
## Survival Months -0.14279002 -0.055980895
summary(Cancer_pca)
## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6
## Standard deviation 1.496 1.0794 0.9892 0.9597 0.71419 0.43317
## Proportion of Variance 0.373 0.1942 0.1631 0.1535 0.08501 0.03127
## Cumulative Proportion 0.373 0.5672 0.7302 0.8837 0.96873 1.00000
# sample scores stored in sparrows_pca$x
# singular values (square roots of eigenvalues) stored in sparrow_pca$sdev
# loadings (eigenvectors) are stored in sparrows_pca$rotation
# variable means stored in sparrows_pca$center
# variable standard deviations stored in sparrows_pca$scale
# A table containing eigenvalues and %'s accounted, follows
# Eigenvalues are sdev^2
(eigen_Cancer <- Cancer_pca$sdev^2)
## [1] 2.2378787 1.1649997 0.9784385 0.9209868 0.5100636 0.1876326
names(eigen_Cancer) <- paste("PC",1:5,sep="")
eigen_Cancer
## PC1 PC2 PC3 PC4 PC5 <NA>
## 2.2378787 1.1649997 0.9784385 0.9209868 0.5100636 0.1876326
sumlambdas <- sum(eigen_Cancer)
sumlambdas
## [1] 6
propvar <- eigen_Cancer/sumlambdas
propvar
## PC1 PC2 PC3 PC4 PC5 <NA>
## 0.37297979 0.19416662 0.16307309 0.15349780 0.08501061 0.03127210
cumvar_Cancer <- cumsum(propvar)
cumvar_Cancer
## PC1 PC2 PC3 PC4 PC5 <NA>
## 0.3729798 0.5671464 0.7302195 0.8837173 0.9687279 1.0000000
matlambdas <- rbind(eigen_Cancer,propvar,cumvar_Cancer)
rownames(matlambdas) <- c("Eigenvalues","Prop. variance","Cum. prop. variance")
round(matlambdas,4)
## PC1 PC2 PC3 PC4 PC5 <NA>
## Eigenvalues 2.2379 1.1650 0.9784 0.9210 0.5101 0.1876
## Prop. variance 0.3730 0.1942 0.1631 0.1535 0.0850 0.0313
## Cum. prop. variance 0.3730 0.5671 0.7302 0.8837 0.9687 1.0000
summary(Cancer_pca)
## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6
## Standard deviation 1.496 1.0794 0.9892 0.9597 0.71419 0.43317
## Proportion of Variance 0.373 0.1942 0.1631 0.1535 0.08501 0.03127
## Cumulative Proportion 0.373 0.5672 0.7302 0.8837 0.96873 1.00000
Cancer_pca$rotation
## PC1 PC2 PC3 PC4
## Age -0.2153849 0.21608166 -0.34917081 -0.88535662
## Stage 0.5628689 -0.32693628 0.06177527 -0.24457235
## Tumor Size 0.5822135 -0.28223117 -0.01433325 -0.21375444
## Regional Node Examined 0.2375181 0.75305159 0.21117279 0.02093686
## Reginol Node Positive 0.4590407 0.43924020 0.01680220 0.01827332
## Survival Months -0.1751633 -0.08214803 0.91059423 -0.33145859
## PC5 PC6
## Age -0.03346239 0.004663803
## Stage 0.18847337 0.690751203
## Tumor Size 0.13490974 -0.719218983
## Regional Node Examined 0.57570300 -0.005676451
## Reginol Node Positive -0.77028208 0.048979548
## Survival Months -0.14279002 -0.055980895
print(Cancer_pca)
## Standard deviations (1, .., p=6):
## [1] 1.4959541 1.0793515 0.9891605 0.9596806 0.7141874 0.4331658
##
## Rotation (n x k) = (6 x 6):
## PC1 PC2 PC3 PC4
## Age -0.2153849 0.21608166 -0.34917081 -0.88535662
## Stage 0.5628689 -0.32693628 0.06177527 -0.24457235
## Tumor Size 0.5822135 -0.28223117 -0.01433325 -0.21375444
## Regional Node Examined 0.2375181 0.75305159 0.21117279 0.02093686
## Reginol Node Positive 0.4590407 0.43924020 0.01680220 0.01827332
## Survival Months -0.1751633 -0.08214803 0.91059423 -0.33145859
## PC5 PC6
## Age -0.03346239 0.004663803
## Stage 0.18847337 0.690751203
## Tumor Size 0.13490974 -0.719218983
## Regional Node Examined 0.57570300 -0.005676451
## Reginol Node Positive -0.77028208 0.048979548
## Survival Months -0.14279002 -0.055980895
## Sample scores stored in sparrow_pca$x
Cancer_pca$x
## PC1 PC2 PC3 PC4 PC5
## [1,] -1.493744354 1.672703734 -0.797771118 -0.639380539 0.852277723
## [2,] 0.426322428 -0.124086338 -0.222112841 0.478038848 -0.014925567
## [3,] 1.694207768 -0.545124348 0.069937198 -1.032701826 -0.039058417
## [4,] -1.767583528 -0.885302494 -0.030847119 -0.208720400 -0.771910136
## [5,] 0.043714825 -1.603388200 -0.903121553 0.849669634 -0.078371793
## [6,] -1.028534021 0.502739380 0.863904840 0.421284750 0.233248754
## [7,] -1.338771984 0.023023987 -0.740136022 1.021953281 0.038121315
## [8,] 0.406514411 -0.944219552 -1.935001240 2.169992691 0.548288673
## [9,] 4.993025728 -0.305103355 0.801778453 0.176933443 -0.724303190
## [10,] 1.937948477 0.689507346 0.639790414 -2.348269489 -0.376692694
## [11,] -1.756901401 0.140915113 -1.036789014 -0.816405788 -0.204199065
## [12,] 1.296312778 -1.473829054 1.127778467 -0.112920985 0.266696937
## [13,] -0.090142691 -0.016296775 -1.070302648 -0.891412586 0.200775716
## [14,] -0.076244034 1.581531699 -0.943407970 1.540387096 0.141353261
## [15,] 1.004107956 1.120512340 -0.515080564 -0.672554789 -1.296448032
## [16,] -1.005634503 0.998331229 -1.092830786 0.057925043 0.742413832
## [17,] -0.538374841 -1.839056096 0.934166263 -0.882076640 -0.578346113
## [18,] 0.204445317 0.244548369 0.249012257 1.256474649 1.134795943
## [19,] -0.419443766 -0.379535399 1.728764442 0.083365143 0.402986436
## [20,] -0.252782392 0.344103196 0.155613436 -0.655869450 0.860603335
## [21,] -0.036353656 -0.349284099 0.645811404 0.425442619 0.372107468
## [22,] 0.504291512 0.121502823 -0.952996651 -0.061329141 0.135596833
## [23,] -0.618672209 -1.285043286 -0.036105811 -0.229784303 -0.280109421
## [24,] 1.459334722 -1.104003050 1.630015919 -0.538883137 1.064729564
## [25,] 0.693501261 3.217631237 1.088615995 -0.680914229 -2.330312186
## [26,] 1.342457422 2.945510521 0.104659090 -0.694326558 -0.785747318
## [27,] 2.475721782 2.107120006 1.821692902 0.042150966 -2.125689786
## [28,] -1.137184838 -0.018509243 0.662500068 1.019754895 0.143564512
## [29,] -0.082096727 0.062026127 -0.404849247 -0.143815038 0.043817854
## [30,] -0.951459346 -0.397603334 0.033425845 -1.324785280 0.016907630
## [31,] 0.004306142 -1.599200390 -0.821234717 0.828802331 -0.096628489
## [32,] -1.358590305 -0.557530387 -1.182191573 0.826013095 -0.330970546
## [33,] -1.790419403 -0.472260893 0.282426323 -0.357402908 -0.542183270
## [34,] -0.908445651 0.994824271 -0.546660828 -0.042005466 0.292432820
## [35,] 1.245709794 0.857794242 -1.178327309 1.397760831 -0.230660457
## [36,] -1.439873416 -0.186081367 0.144133667 0.662537801 -0.393665514
## [37,] 0.636390371 0.900377415 -1.197745317 0.553485818 0.437914429
## [38,] -1.304428696 0.097530771 1.328492259 0.221100925 -0.155155562
## [39,] -0.097417933 -0.858136005 0.513336501 0.257353363 0.029439452
## [40,] -0.188925650 -0.025716107 1.521237025 -0.147451873 -0.286733286
## [41,] 2.535953943 -0.283072938 -1.273811462 -0.496124138 -0.691155605
## [42,] -1.364589888 0.380987232 -0.926166470 -0.409214549 -0.084453563
## [43,] -1.095258604 -1.245692755 -0.025636708 -0.959504567 -0.544787256
## [44,] 0.018958421 0.185171532 0.594724325 -0.026225609 -0.312285920
## [45,] -1.483766860 0.205593899 -0.521531513 0.532329976 -0.202487124
## [46,] 0.803570710 -0.823728790 0.269737583 -1.940110944 -0.213877418
## [47,] -0.776759752 0.318065419 -0.898736044 2.118307298 0.308120927
## [48,] -1.440160549 0.277491231 -0.933452622 -0.172656258 0.076695703
## [49,] 0.550199236 0.443259288 0.544534206 -0.061726221 -0.634281043
## [50,] -1.959716237 0.269905907 -0.358261698 -1.104900464 -0.742921582
## [51,] 0.283946083 -0.215989222 0.718462913 1.705505213 0.429398197
## [52,] 0.584420507 -1.170636855 -0.658910102 -2.000608348 0.454750957
## [53,] 2.164109035 -2.375151885 0.202704168 -1.926001263 0.605914036
## [54,] 1.673683848 -0.438611018 -0.189966395 -1.566014043 1.244480037
## [55,] -1.630123732 0.631351549 -0.019980046 0.212113815 0.215871580
## [56,] -1.450559221 0.201501035 -0.069005014 0.333630589 0.063005452
## [57,] -0.534036352 0.291756051 0.624478817 -1.023860005 0.669994233
## [58,] -0.354843129 3.274197111 2.410035980 0.361353654 2.502769179
## [59,] -1.178588655 0.226034827 0.171909908 0.786762124 0.247357475
## [60,] -1.248535425 0.638963394 0.202025885 0.279803670 0.179044984
## [61,] -0.944827480 1.241989527 0.467351263 0.104831170 0.693575290
## [62,] -1.056029210 0.031887224 -0.922233051 1.020017722 0.191600412
## [63,] -0.473763736 -1.839525046 0.381440310 1.043813308 -0.465299021
## [64,] 1.681009012 -0.528168820 0.166784745 -1.236306623 1.216190250
## [65,] -1.312786276 0.965097163 -0.969708882 -0.635102168 0.024970627
## [66,] -1.639877002 -0.931529988 1.401477586 0.658502060 -0.668767345
## [67,] 4.455166578 1.087532562 0.124772958 2.053348449 -1.489900944
## [68,] -0.707613499 0.590986037 1.179291019 1.595111891 0.263308423
## [69,] -1.710632794 -0.549715482 -0.153074842 -0.100695874 -0.540451474
## [70,] -1.171903123 0.100583865 0.469100757 0.412780064 -0.339388614
## [71,] 3.302612150 -1.737283578 1.502810946 -1.179097587 -0.118238924
## [72,] 2.121655213 2.644141124 -2.473204090 -0.044893038 -1.314192531
## [73,] 0.528823585 -0.636078944 0.137430927 2.495082814 0.843161685
## [74,] -1.868775707 0.569029628 0.581800057 -1.084485611 0.002065102
## [75,] 0.683905846 1.767290796 0.241693051 -1.337566812 -1.608284497
## [76,] 0.821006546 -1.188104492 0.917466077 -1.089980478 0.637354405
## [77,] -0.499967072 -0.063567628 -0.217092609 -1.242667319 -0.300754296
## [78,] 0.056071716 -1.653376800 1.664161542 0.435774870 -0.079376450
## [79,] 0.099588612 -1.161140621 0.358003056 -0.058098223 0.191212303
## [80,] -1.638985742 0.150875793 -1.403816856 -0.700686152 -0.135813445
## [81,] 0.865297254 1.214733944 1.463461173 -0.297882350 -1.014695877
## [82,] -1.545124764 0.127252910 -0.935729044 -0.793110208 -0.096332740
## [83,] -0.757282603 -0.365269832 -0.559376514 -1.125365040 -0.112495907
## [84,] -1.494668798 -0.862217669 -1.017557513 0.729371690 -0.585327071
## [85,] -1.198962297 0.090483632 -0.244225721 0.803338834 0.150630291
## [86,] 1.053228198 0.023027292 0.260206980 0.703883631 -1.086933498
## [87,] 2.839883593 -2.296312935 0.510353279 -0.693661524 0.066738128
## [88,] 1.506058603 -1.812772768 0.528733408 -0.767001468 0.643656650
## [89,] -1.539415867 -0.136768478 0.768955037 -0.049503375 -0.188258747
## [90,] -2.166532837 0.071753733 0.343483494 -0.898166612 -0.445936393
## [91,] 0.893002750 -1.772886261 0.734063638 -0.797845672 0.341156668
## [92,] -0.677904182 -0.104397875 0.169469929 2.673756815 0.405882517
## [93,] -0.646604416 -0.740495104 0.063231982 -1.095809541 -0.767513218
## [94,] 1.683330979 1.567742424 -0.698706197 1.431672587 -1.080548515
## [95,] -1.509921397 0.297490480 0.490010821 -0.323083740 -0.437095352
## [96,] -0.135237286 0.293266912 -1.015571227 -0.225694168 0.642455326
## [97,] 0.027644129 -1.133291443 -1.997458759 1.032137750 -0.070625404
## [98,] -0.637273583 -0.513850978 -0.306967375 -0.684532247 0.140054208
## [99,] 1.070049729 -2.036508976 -0.316339810 -0.094341352 -0.094161935
## [100,] -0.455435814 0.089328755 -1.403983913 -1.027093674 0.560281943
## [101,] 4.600390311 2.244846920 0.532264308 1.259266636 -1.010942778
## [102,] -0.787145836 1.086091949 0.549806202 1.093912587 0.984179992
## [103,] 0.655142324 -1.683984928 -2.308143986 2.208715115 0.240582243
## [104,] -0.428540034 -0.840500324 -1.048098702 -0.027665882 0.077046929
## [105,] -0.110654721 -0.123171275 -0.175937919 0.338031509 0.196792323
## [106,] -0.734249607 -1.236231879 -1.090037416 -0.386975718 -0.336972535
## [107,] 0.296584193 -0.577728068 -2.014640498 0.588158511 0.632602330
## [108,] -1.410702952 0.429684625 -0.958296105 -0.866024725 -0.101651534
## [109,] -0.418905210 -1.232525386 1.863199813 1.081316900 -0.304585111
## [110,] 0.446752555 1.508585940 -0.342268303 -0.736468382 1.406332814
## [111,] -1.134059417 0.782686222 -0.521004605 -0.152263500 -0.210024740
## [112,] 1.181466882 -2.299898160 0.735344703 0.997333267 -0.237945040
## [113,] 1.830654533 1.883074076 0.954309940 0.626252247 0.685943765
## [114,] 0.454774207 -0.643039459 0.237045213 0.759165544 0.470129822
## [115,] 0.864920996 -1.531113286 1.149483739 -0.984234084 -0.541097522
## [116,] -0.897625868 0.218458064 -0.870977930 0.772271080 -0.128040261
## [117,] 1.357865125 -1.941049776 0.946671254 -0.674767960 0.499517827
## [118,] -0.915336154 1.327339693 0.352068802 -1.370754921 -1.073206670
## [119,] 0.094948933 -0.356826249 1.052712045 0.237447671 0.183785081
## [120,] -0.037442692 -0.108870167 -0.518461408 0.323952099 0.490323176
## [121,] -0.703244230 -0.760629115 0.236405707 -1.666145723 -0.328854978
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## [183,] -1.497163756 -0.391927377 -2.671606811 0.257351508 -0.356818941
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## [186,] -0.646848816 0.019961075 0.140097904 -1.345604301 0.174968361
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## [189,] 0.597265999 2.425823378 1.007898127 -0.923443496 0.528966635
## [190,] -1.161264597 0.015537197 0.541717900 1.081599330 0.151672237
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## [199,] 0.296675856 0.507260694 -0.459773048 0.471858283 1.040250209
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## [202,] -0.085308348 0.324848824 -0.506897761 -0.413457726 0.183316995
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## [211,] 1.978468906 -1.541564858 0.344229726 0.254916972 0.343867249
## [212,] 2.937647970 0.023153745 -1.467099553 2.004769891 -0.185012738
## [213,] -0.086636710 1.891839624 1.573096232 0.223299508 -2.221106615
## [214,] -1.481813930 0.006331169 -1.173928063 -0.250137785 -0.112924714
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## [219,] -1.586401627 -0.388025617 -1.097489991 -0.453696582 -0.661613141
## [220,] 4.773395918 2.278577670 -1.336404778 0.510730406 -1.718160684
## [221,] 2.921320323 -0.012042086 -1.874368061 -0.045263697 -0.566144677
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## [223,] -1.241990069 0.411074638 1.790709487 0.707551103 0.092693855
## [224,] -0.133856941 -0.846749537 0.481837944 1.031203316 -0.200664046
## [225,] -1.486223026 -1.226757723 0.663500601 1.212738370 -0.747306389
## [226,] -0.762041381 1.164340422 1.896521625 1.074683686 0.812249845
## [227,] 2.005021660 0.341436716 -0.409217808 -0.832010193 0.147847697
## [228,] 1.814305601 1.684900471 0.545885187 -0.444700098 2.887385706
## [229,] -1.411373860 -0.029800132 -1.219717248 -0.012627251 -0.086502351
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## [232,] -1.210396528 0.443593233 -1.157566359 -0.418875718 -1.229168913
## [233,] 0.367888943 1.034558583 -0.899804344 -1.320083756 0.545063435
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## [236,] -1.290446225 1.701929130 -0.262965485 -0.898972118 0.974935670
## [237,] 3.655612544 1.679581237 -0.078271387 0.366568656 -1.144046957
## [238,] 0.611276361 -1.193837776 1.025840807 -1.693775105 0.496074659
## [239,] 6.711875034 1.215508748 -1.279625142 0.587766000 -0.938041730
## [240,] -1.281390399 -0.456797389 0.383696463 1.327109609 -0.434647734
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## [242,] 0.008347450 1.173046306 1.625650682 -0.126758712 1.284764016
## [243,] -0.958826089 -0.492058288 0.745646701 -1.985299776 -0.313503201
## [244,] 1.609087788 0.768291741 1.106856868 1.288165361 -1.317902920
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## [248,] 0.486998129 0.122844418 -0.822868404 1.350720580 0.697385548
## [249,] -0.821657492 -0.011924402 0.873543779 1.971662603 0.110811955
## [250,] -1.398504155 -0.243599402 0.837410828 0.477686433 -0.150887846
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## [253,] -0.289560811 -1.753881720 0.731478923 1.008115634 -0.564319747
## [254,] 2.350354264 -1.374432502 0.783487702 1.516771930 0.201694966
## [255,] 2.529945185 -0.796264796 -1.084229732 -1.768591624 1.468016449
## [256,] -0.594294620 0.606268901 0.546284310 -1.512570945 0.547901821
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## [260,] -0.286827613 -0.440600376 -0.511227621 -0.188717119 0.390008978
## [261,] -0.645411407 0.058506107 -2.305257330 2.581332331 0.223956712
## [262,] -0.628353063 -1.040695063 1.499765220 0.328717274 -0.091370940
## [263,] -0.136446586 -0.912547265 0.240795333 0.609862680 -0.011841605
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## [267,] -0.854919366 2.319121839 -0.534036982 -0.401249649 1.590398378
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## [270,] -0.346935263 1.923554748 -1.292856361 -0.360145431 -0.649527552
## [271,] 2.611945346 -0.868543943 -0.456914061 1.833405222 -0.121158473
## [272,] -0.054669716 0.467014101 -0.459580646 0.187565076 0.815668207
## [273,] 0.590763284 0.081986670 -0.821826225 1.066920091 0.715892272
## [274,] -0.771766282 0.497567733 -0.144543170 -0.043136586 -1.433593942
## [275,] 0.287407340 -0.999343796 -0.141647094 1.726767706 0.460339894
## [276,] -1.904210848 -0.711924915 -0.636156799 0.229311959 -0.732363166
## [277,] 1.980934953 -2.144737237 -1.558960290 -1.734660915 0.372677052
## [278,] 4.349982486 0.818990696 -1.850629065 0.156456507 -0.310120302
## [279,] -1.601460087 0.466219801 0.555412046 -1.282120597 -0.177034377
## [280,] 1.110817200 -0.894199685 0.626718163 -1.090577512 0.457144316
## [281,] -1.635586546 0.585764692 0.351472824 -0.436299965 0.162468184
## [282,] -0.910449829 -0.063109780 -0.243265787 1.440217859 -0.008738371
## [283,] 0.979721615 0.904442368 -1.232199254 1.008144535 -0.363957491
## [284,] -0.472435837 -0.521473629 0.942802823 0.140237047 0.029009438
## [285,] 0.298128461 -0.439838094 -0.230211394 0.045875504 0.466431500
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## [288,] 0.489276289 0.149716001 1.343990756 -0.776952747 -1.363924275
## [289,] 1.167193218 4.324487587 0.744165112 -1.104452819 -2.960549114
## [290,] 5.639123713 1.493129585 0.436631086 0.391589194 1.328124017
## [291,] 0.076038156 2.149080398 1.231684279 -0.889701456 2.108001645
## [292,] -1.306362503 0.777428880 -0.836033189 -0.505010722 0.429704777
## [293,] -1.492629535 0.346667458 -1.594060891 -0.744201427 0.053005921
## [294,] 0.548191410 0.159332266 1.521957843 0.691090269 0.002822644
## [295,] 3.173294742 -0.713640891 1.483201289 -0.597042450 -0.955008287
## [296,] -1.711510331 0.207909220 -0.931632873 -0.732023246 -0.134887380
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## [299,] -1.338159554 0.850035604 0.991498508 0.275292019 0.519975147
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## [302,] 0.451358041 0.509847268 -0.404959275 1.025191596 1.150524367
## [303,] -0.410664267 1.809811675 0.163254213 1.203959868 1.107465182
## [304,] 0.631511135 4.553878477 0.617849698 -0.258625983 0.452803511
## [305,] 0.606275351 1.307303704 -1.190130416 -1.085147986 0.839582865
## [306,] 3.760469200 -1.318016453 -1.571659239 -0.958198521 -0.168654341
## [307,] 0.283257978 0.334225557 0.900109850 1.387190281 0.742119351
## [308,] 1.205872572 -1.025116718 -0.694241491 -0.489820821 0.185091372
## [309,] -0.547890175 -1.378267017 0.199506501 0.006777245 -0.282776412
## [310,] 0.675442079 -0.040092847 0.040280714 1.538300103 0.724233244
## [311,] -0.347420655 -1.297275709 -0.084885546 0.216594996 -0.374740492
## [312,] -1.082694803 1.058501944 -1.274637266 -0.535652316 -0.301170989
## [313,] -0.809911038 0.678119879 -0.193503870 0.489931605 -0.567989774
## [314,] 2.814192996 1.465015414 1.296910650 -1.024401483 -0.754090861
## [315,] -1.219216145 -0.216402526 0.775638956 0.706433637 -0.029531003
## [316,] -0.839858529 -1.160921154 -0.067522123 -0.376613864 -0.332337533
## [317,] 1.906604890 -1.476681383 -0.028831221 0.037013607 1.083914038
## [318,] -1.128786006 0.395890021 0.040446729 0.390323605 -0.149885563
## [319,] 4.980287452 1.400993226 0.386980437 0.646687478 -1.083846603
## [320,] -0.396555408 -0.215395452 -1.222389233 -0.813225124 0.424557329
## [321,] -1.686147468 0.664222126 1.210799613 -0.375476795 0.198108774
## [322,] -0.771587552 0.001912498 -0.021523533 2.182231316 0.393142757
## [323,] 2.121003409 -2.080663494 0.161998088 0.897550000 0.380306029
## [324,] 0.183525269 0.711131176 0.676974276 -0.837925098 -0.201495035
## [325,] -0.388480855 -0.019183155 -0.034180507 -0.379134234 0.583222451
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## [327,] -0.016309255 -0.272150173 1.123754077 -0.347941297 -0.103237180
## [328,] -1.509365115 -1.227221931 0.110956778 1.437386493 -0.758506439
## [329,] 1.128006246 -1.746278013 0.499382396 -1.619420542 0.555724903
## [330,] -0.013678857 0.097843119 0.408072714 -0.795855347 -1.175223096
## [331,] 0.134239505 0.261168839 1.687827776 0.217195174 1.082628063
## [332,] 0.543266130 0.289044087 -1.889627887 1.415180585 1.063577278
## [333,] -1.694510184 -0.384164773 0.978956440 -0.619188118 -0.943767153
## [334,] -1.177192240 0.755347480 -0.072837954 0.262273753 0.532730202
## [335,] -0.154704801 -0.482019591 -0.130393501 0.108703255 0.455787032
## [336,] -1.222393212 -0.140605864 0.470903440 0.854635087 -0.236602493
## [337,] 0.985284375 -2.085350193 -0.309169317 -0.356636930 0.209646403
## [338,] 1.845084419 -1.284127961 -0.428328294 -1.460289251 0.838247554
## [339,] -1.537001279 1.111570387 0.652894920 -1.060718845 -0.002140100
## [340,] 0.486580696 -0.438599188 -0.143918334 0.966749788 0.107166844
## [341,] -0.381846642 -0.365594889 0.626052636 0.039508221 -0.092159877
## [342,] -1.058469609 1.839970213 -0.254329772 -0.731552164 -0.827823834
## [343,] 1.953784231 -1.229071105 0.160259672 0.867246394 1.295990204
## [344,] -1.632770525 -0.310017947 0.586575867 0.624972262 -0.312659105
## [345,] -0.069211481 1.179578849 -0.019456868 -1.025693279 0.424192027
## [346,] 0.924645953 0.318200997 -0.038558980 -0.176342543 -1.278270521
## [347,] -1.679627649 -0.870249748 1.201962925 0.638583744 -0.657934688
## [348,] -0.138978457 -0.327879510 1.445999742 0.018109114 0.324021275
## [349,] -0.306354427 2.443421548 0.256738595 0.723881262 0.004780055
## [350,] -1.082397105 0.511694553 0.396630701 0.376171916 0.200267508
## [351,] 1.560087096 -0.172608049 2.042673531 0.001387343 0.943307040
## [352,] 0.213890453 0.121650120 -0.363220480 0.143134581 0.251009799
## [353,] -1.243101129 -0.469575151 -1.404226113 1.148855158 -0.206147146
## [354,] -1.723673624 -0.628891973 1.215101216 0.822337346 -0.530509884
## [355,] -1.845736715 -1.246640827 1.218806001 0.592440275 -0.970712299
## [356,] -0.533908899 0.509703545 -1.010222476 -1.067833304 0.770760459
## [357,] -0.621852817 1.060330174 -0.185420284 0.974853637 0.788314716
## [358,] -0.663822556 -0.698693563 -1.437208451 -1.000964685 -0.267520648
## [359,] -1.464448793 -0.997923794 0.090438438 0.991886193 -0.619748924
## [360,] -1.523194528 1.088366756 -0.015584201 -1.071387626 0.484479318
## [361,] -0.249284791 -0.495162923 -0.888175969 0.194375075 0.137323234
## [362,] -0.978278825 0.745196276 1.673492426 0.624652999 0.677279063
## [363,] 2.298810986 -0.090143085 -0.751106742 -0.561856912 1.569191798
## [364,] -0.641761160 -1.573225212 0.960424847 -0.179437036 -0.696431558
## [365,] -1.237501132 -0.412442737 1.793811573 1.137104529 -0.371283677
## [366,] -1.157403928 0.923508573 -0.442026074 -0.884941552 -0.171459484
## [367,] -0.796933393 1.222876039 0.723404723 -0.237384378 -0.510118334
## [368,] 2.646899548 0.301553970 0.690593527 -2.443750630 0.663805037
## [369,] -0.178975454 -0.138624086 1.105283992 -1.499072183 -0.164055484
## [370,] -1.330874437 0.769296425 -0.127097036 -1.223980155 -0.869663470
## [371,] 0.785519987 2.132318925 0.981263612 -0.639682484 -0.035075161
## [372,] 4.528600634 -0.995996130 0.568209680 -0.292649916 -0.397415282
## [373,] -2.215387412 -0.717213408 0.437807288 -1.098624561 -0.945243579
## [374,] 0.852816653 0.697424945 -0.415247520 0.859928559 0.964247801
## [375,] 1.528575274 1.579100810 0.424898608 1.740887715 -0.368739736
## [376,] 1.052831636 0.469776583 0.746395631 -0.477473960 -1.373515237
## [377,] 3.308075529 -0.637217047 -0.361014725 -0.281269186 -0.462933899
## [378,] 0.145308323 -0.337470348 1.183817291 1.285154406 0.271835930
## [379,] -0.100434292 -0.148112235 0.886936726 0.259148546 0.704812541
## PC6
## [1,] 0.116709537
## [2,] 0.110173000
## [3,] 0.151011377
## [4,] -0.343807479
## [5,] -0.068417317
## [6,] -0.420280958
## [7,] 0.014839886
## [8,] 0.336718257
## [9,] -0.045952454
## [10,] 1.939826284
## [11,] -0.146897222
## [12,] 0.183314250
## [13,] 0.114162471
## [14,] -0.102727402
## [15,] 0.196911289
## [16,] -0.296960713
## [17,] -0.346683316
## [18,] 0.385229903
## [19,] 0.250212417
## [20,] 0.210997273
## [21,] 0.178758339
## [22,] -0.003801151
## [23,] 0.217319459
## [24,] -0.187966712
## [25,] -0.249408299
## [26,] 0.582504343
## [27,] -0.264956027
## [28,] -0.324073726
## [29,] 0.392690074
## [30,] 0.433561922
## [31,] -0.044052794
## [32,] -0.172924722
## [33,] -0.273046392
## [34,] -0.339264995
## [35,] 0.377235819
## [36,] -0.090271827
## [37,] 0.414287669
## [38,] -0.393701821
## [39,] 0.033505637
## [40,] 0.354862667
## [41,] 0.077217544
## [42,] -0.251343699
## [43,] 0.437209594
## [44,] 0.418033744
## [45,] 0.092143326
## [46,] 0.453442755
## [47,] 0.025217332
## [48,] -0.198309910
## [49,] 0.187074835
## [50,] 0.063584865
## [51,] 0.411945392
## [52,] 0.347020693
## [53,] -1.602200768
## [54,] -0.297652746
## [55,] 0.140534670
## [56,] -0.120117267
## [57,] 0.295188323
## [58,] -0.436240290
## [59,] -0.241532009
## [60,] -0.152644965
## [61,] -0.340782009
## [62,] -0.237639469
## [63,] 0.300926071
## [64,] -0.253457399
## [65,] -0.123036265
## [66,] -0.318934216
## [67,] 0.157579795
## [68,] -0.260813996
## [69,] -0.245354609
## [70,] -0.305254302
## [71,] -1.882250425
## [72,] 0.409598000
## [73,] 0.232202465
## [74,] -0.149057573
## [75,] 0.545903188
## [76,] 0.277588617
## [77,] 0.361912198
## [78,] -0.478016137
## [79,] -0.412381253
## [80,] -0.183130748
## [81,] 0.233456245
## [82,] -0.356154388
## [83,] 0.449569521
## [84,] -0.185788498
## [85,] -0.219609958
## [86,] -0.001711114
## [87,] -1.559617792
## [88,] -0.428893296
## [89,] -0.349853393
## [90,] 0.067731920
## [91,] 0.142796842
## [92,] -0.180830638
## [93,] 0.315292384
## [94,] 0.557663845
## [95,] -0.172373827
## [96,] 0.407727459
## [97,] 0.327538602
## [98,] 0.346056104
## [99,] 2.163269668
## [100,] 0.345529449
## [101,] 0.138719045
## [102,] -0.279523523
## [103,] -0.084975054
## [104,] 0.337408982
## [105,] 0.436700603
## [106,] 0.388716289
## [107,] 0.023800405
## [108,] -0.344894615
## [109,] 0.380430817
## [110,] 0.059212100
## [111,] -0.160062648
## [112,] 0.451808896
## [113,] -0.328134576
## [114,] -0.232509061
## [115,] 0.417691744
## [116,] -0.283499777
## [117,] -0.334241319
## [118,] -0.354492127
## [119,] 0.016626218
## [120,] 0.329368287
## [121,] 0.014802916
## [122,] 1.788209994
## [123,] -0.225290106
## [124,] -0.049381001
## [125,] -0.176037238
## [126,] -0.147416810
## [127,] 0.274931744
## [128,] -0.288402296
## [129,] -0.238830171
## [130,] -0.321394130
## [131,] -0.060804904
## [132,] -0.198430755
## [133,] -0.201882037
## [134,] -0.416230299
## [135,] -0.104823016
## [136,] -0.259292999
## [137,] 0.309515655
## [138,] 0.473433423
## [139,] -0.224455247
## [140,] -0.113549634
## [141,] -0.029270791
## [142,] -0.408139727
## [143,] -0.249679273
## [144,] 0.052432954
## [145,] 0.123609326
## [146,] 0.110721474
## [147,] 0.039482206
## [148,] -0.055563924
## [149,] -0.301541438
## [150,] 0.339761189
## [151,] -0.143565175
## [152,] 0.495882321
## [153,] -0.338275303
## [154,] -0.259013852
## [155,] -0.268105530
## [156,] -0.980893416
## [157,] -0.246803124
## [158,] -0.078306763
## [159,] 0.382030122
## [160,] 0.087323777
## [161,] 0.376505108
## [162,] 0.053401289
## [163,] -0.338300621
## [164,] -0.183747770
## [165,] 0.432642111
## [166,] 0.187719391
## [167,] -0.323645603
## [168,] 0.829006715
## [169,] 0.043491740
## [170,] -0.248046133
## [171,] -0.060255793
## [172,] -0.083545793
## [173,] -0.167508321
## [174,] -0.089468938
## [175,] -0.143831223
## [176,] 0.323860642
## [177,] -0.174432941
## [178,] -0.239734115
## [179,] 0.497289814
## [180,] -0.327540210
## [181,] -0.151688764
## [182,] 0.197182238
## [183,] -0.042715485
## [184,] 0.044010655
## [185,] -0.925270972
## [186,] 0.322942444
## [187,] -0.036587651
## [188,] 0.356359819
## [189,] 0.423139332
## [190,] -0.257850948
## [191,] 0.463686146
## [192,] -0.032295644
## [193,] -0.221120598
## [194,] 0.347410914
## [195,] -0.102882758
## [196,] -0.052886406
## [197,] 0.099771649
## [198,] 0.161046943
## [199,] 0.245795874
## [200,] 0.272924190
## [201,] 0.339839246
## [202,] 0.395294558
## [203,] -0.065386536
## [204,] 0.561844444
## [205,] -0.271407182
## [206,] -0.059059407
## [207,] 0.083045883
## [208,] 0.377344777
## [209,] 0.334594979
## [210,] 2.210117773
## [211,] -0.225352991
## [212,] 0.659498155
## [213,] 0.005821771
## [214,] -0.246898562
## [215,] 0.168733702
## [216,] -0.366893261
## [217,] -0.293117425
## [218,] 0.423293245
## [219,] -0.277523269
## [220,] 0.108760866
## [221,] 0.070710680
## [222,] 0.163384108
## [223,] -0.232906221
## [224,] 0.408184032
## [225,] -0.300209061
## [226,] -0.343281023
## [227,] 0.380266460
## [228,] 0.475769439
## [229,] -0.240418547
## [230,] 0.118544474
## [231,] 0.411577815
## [232,] -0.017746096
## [233,] -0.022662183
## [234,] -0.215224961
## [235,] -0.336453644
## [236,] -0.208327609
## [237,] 0.415886191
## [238,] 0.260849310
## [239,] -0.336942900
## [240,] -0.122484819
## [241,] -0.025660118
## [242,] 0.330693931
## [243,] 0.187450418
## [244,] 0.092254142
## [245,] -0.103389100
## [246,] -0.135338511
## [247,] -0.081072198
## [248,] 0.345962874
## [249,] -0.250967381
## [250,] -0.344899324
## [251,] -0.429960219
## [252,] -0.282830186
## [253,] 0.174435063
## [254,] -0.002994835
## [255,] -1.217412358
## [256,] 0.360421127
## [257,] -0.146287428
## [258,] -0.133025274
## [259,] -0.126146676
## [260,] 0.220778323
## [261,] 0.108029807
## [262,] 0.349752615
## [263,] 0.200005121
## [264,] -0.101933578
## [265,] -0.161334026
## [266,] 0.285586865
## [267,] -0.238563544
## [268,] 0.083679922
## [269,] 0.509906873
## [270,] -0.146139621
## [271,] 0.334416111
## [272,] 0.473647831
## [273,] 0.136442835
## [274,] -0.251405937
## [275,] 0.114366181
## [276,] 0.048022334
## [277,] -1.054946234
## [278,] -0.700681151
## [279,] -0.434292485
## [280,] 0.255500421
## [281,] -0.124820953
## [282,] -0.258508925
## [283,] 0.519297048
## [284,] 0.418680932
## [285,] -0.218443452
## [286,] -0.216123751
## [287,] 0.115923969
## [288,] -0.027866918
## [289,] -0.058716464
## [290,] -2.000384525
## [291,] 0.277974900
## [292,] -0.293421787
## [293,] -0.259635342
## [294,] 0.059625913
## [295,] 0.971487465
## [296,] -0.150615259
## [297,] -0.400937784
## [298,] 0.238954410
## [299,] -0.144937084
## [300,] 0.201952185
## [301,] -0.447834040
## [302,] 0.281901496
## [303,] -0.203869133
## [304,] -0.134202490
## [305,] -0.059036104
## [306,] -1.689975498
## [307,] 0.458648969
## [308,] 0.521154125
## [309,] 0.178933466
## [310,] 0.097184547
## [311,] 0.178727506
## [312,] -0.114849810
## [313,] -0.177928676
## [314,] 0.278091472
## [315,] -0.424718686
## [316,] 0.421376781
## [317,] -0.381796482
## [318,] -0.221941061
## [319,] -0.754255469
## [320,] 0.249838558
## [321,] -0.111526776
## [322,] -0.207650126
## [323,] -0.362767449
## [324,] 0.207891984
## [325,] 0.340268457
## [326,] 0.368766457
## [327,] 0.012058601
## [328,] -0.149559490
## [329,] 1.463155184
## [330,] 0.382942476
## [331,] -0.032112095
## [332,] 0.397084457
## [333,] -0.354911460
## [334,] -0.233823936
## [335,] 0.146812456
## [336,] -0.250028422
## [337,] 0.205107833
## [338,] -0.667916271
## [339,] -0.159417162
## [340,] 0.044940196
## [341,] 0.444365443
## [342,] 0.218371896
## [343,] -0.083864131
## [344,] -0.066718642
## [345,] 0.460637350
## [346,] 0.010040209
## [347,] -0.249703684
## [348,] 0.069849151
## [349,] 0.133553509
## [350,] -0.337335972
## [351,] 0.358285729
## [352,] 0.221064477
## [353,] -0.125296735
## [354,] -0.070458295
## [355,] -0.224997131
## [356,] 0.501370980
## [357,] -0.349367892
## [358,] 0.380452253
## [359,] -0.271394600
## [360,] -0.258419685
## [361,] 0.402658885
## [362,] -0.468027915
## [363,] -0.324990632
## [364,] 0.142034987
## [365,] -0.347928412
## [366,] -0.351391164
## [367,] -0.285977778
## [368,] -0.971457197
## [369,] -0.181523245
## [370,] -0.240725882
## [371,] 0.387573331
## [372,] -0.229079837
## [373,] -0.209054420
## [374,] 0.036780440
## [375,] 0.503922523
## [376,] -0.173505314
## [377,] -0.787406645
## [378,] 0.319960047
## [379,] 0.154968029
# Identifying the scores by their survival status
sparrtyp_pca <- cbind(data.frame(Cancer$Survivor),Cancer_pca$x)
sparrtyp_pca
## Cancer.Survivor PC1 PC2 PC3 PC4
## 1 Alive -1.493744354 1.672703734 -0.797771118 -0.639380539
## 2 Alive 0.426322428 -0.124086338 -0.222112841 0.478038848
## 3 Alive 1.694207768 -0.545124348 0.069937198 -1.032701826
## 4 Alive -1.767583528 -0.885302494 -0.030847119 -0.208720400
## 5 Alive 0.043714825 -1.603388200 -0.903121553 0.849669634
## 6 Alive -1.028534021 0.502739380 0.863904840 0.421284750
## 7 Alive -1.338771984 0.023023987 -0.740136022 1.021953281
## 8 Dead 0.406514411 -0.944219552 -1.935001240 2.169992691
## 9 Alive 4.993025728 -0.305103355 0.801778453 0.176933443
## 10 Alive 1.937948477 0.689507346 0.639790414 -2.348269489
## 11 Dead -1.756901401 0.140915113 -1.036789014 -0.816405788
## 12 Alive 1.296312778 -1.473829054 1.127778467 -0.112920985
## 13 Alive -0.090142691 -0.016296775 -1.070302648 -0.891412586
## 14 Alive -0.076244034 1.581531699 -0.943407970 1.540387096
## 15 Alive 1.004107956 1.120512340 -0.515080564 -0.672554789
## 16 Alive -1.005634503 0.998331229 -1.092830786 0.057925043
## 17 Alive -0.538374841 -1.839056096 0.934166263 -0.882076640
## 18 Alive 0.204445317 0.244548369 0.249012257 1.256474649
## 19 Alive -0.419443766 -0.379535399 1.728764442 0.083365143
## 20 Alive -0.252782392 0.344103196 0.155613436 -0.655869450
## 21 Alive -0.036353656 -0.349284099 0.645811404 0.425442619
## 22 Alive 0.504291512 0.121502823 -0.952996651 -0.061329141
## 23 Alive -0.618672209 -1.285043286 -0.036105811 -0.229784303
## 24 Alive 1.459334722 -1.104003050 1.630015919 -0.538883137
## 25 Alive 0.693501261 3.217631237 1.088615995 -0.680914229
## 26 Alive 1.342457422 2.945510521 0.104659090 -0.694326558
## 27 Alive 2.475721782 2.107120006 1.821692902 0.042150966
## 28 Alive -1.137184838 -0.018509243 0.662500068 1.019754895
## 29 Alive -0.082096727 0.062026127 -0.404849247 -0.143815038
## 30 Alive -0.951459346 -0.397603334 0.033425845 -1.324785280
## 31 Alive 0.004306142 -1.599200390 -0.821234717 0.828802331
## 32 Alive -1.358590305 -0.557530387 -1.182191573 0.826013095
## 33 Alive -1.790419403 -0.472260893 0.282426323 -0.357402908
## 34 Alive -0.908445651 0.994824271 -0.546660828 -0.042005466
## 35 Alive 1.245709794 0.857794242 -1.178327309 1.397760831
## 36 Alive -1.439873416 -0.186081367 0.144133667 0.662537801
## 37 Alive 0.636390371 0.900377415 -1.197745317 0.553485818
## 38 Alive -1.304428696 0.097530771 1.328492259 0.221100925
## 39 Alive -0.097417933 -0.858136005 0.513336501 0.257353363
## 40 Alive -0.188925650 -0.025716107 1.521237025 -0.147451873
## 41 Dead 2.535953943 -0.283072938 -1.273811462 -0.496124138
## 42 Alive -1.364589888 0.380987232 -0.926166470 -0.409214549
## 43 Alive -1.095258604 -1.245692755 -0.025636708 -0.959504567
## 44 Alive 0.018958421 0.185171532 0.594724325 -0.026225609
## 45 Alive -1.483766860 0.205593899 -0.521531513 0.532329976
## 46 Alive 0.803570710 -0.823728790 0.269737583 -1.940110944
## 47 Dead -0.776759752 0.318065419 -0.898736044 2.118307298
## 48 Alive -1.440160549 0.277491231 -0.933452622 -0.172656258
## 49 Alive 0.550199236 0.443259288 0.544534206 -0.061726221
## 50 Alive -1.959716237 0.269905907 -0.358261698 -1.104900464
## 51 Alive 0.283946083 -0.215989222 0.718462913 1.705505213
## 52 Alive 0.584420507 -1.170636855 -0.658910102 -2.000608348
## 53 Alive 2.164109035 -2.375151885 0.202704168 -1.926001263
## 54 Alive 1.673683848 -0.438611018 -0.189966395 -1.566014043
## 55 Alive -1.630123732 0.631351549 -0.019980046 0.212113815
## 56 Alive -1.450559221 0.201501035 -0.069005014 0.333630589
## 57 Alive -0.534036352 0.291756051 0.624478817 -1.023860005
## 58 Alive -0.354843129 3.274197111 2.410035980 0.361353654
## 59 Alive -1.178588655 0.226034827 0.171909908 0.786762124
## 60 Alive -1.248535425 0.638963394 0.202025885 0.279803670
## 61 Alive -0.944827480 1.241989527 0.467351263 0.104831170
## 62 Alive -1.056029210 0.031887224 -0.922233051 1.020017722
## 63 Alive -0.473763736 -1.839525046 0.381440310 1.043813308
## 64 Alive 1.681009012 -0.528168820 0.166784745 -1.236306623
## 65 Dead -1.312786276 0.965097163 -0.969708882 -0.635102168
## 66 Alive -1.639877002 -0.931529988 1.401477586 0.658502060
## 67 Dead 4.455166578 1.087532562 0.124772958 2.053348449
## 68 Alive -0.707613499 0.590986037 1.179291019 1.595111891
## 69 Alive -1.710632794 -0.549715482 -0.153074842 -0.100695874
## 70 Alive -1.171903123 0.100583865 0.469100757 0.412780064
## 71 Alive 3.302612150 -1.737283578 1.502810946 -1.179097587
## 72 Dead 2.121655213 2.644141124 -2.473204090 -0.044893038
## 73 Alive 0.528823585 -0.636078944 0.137430927 2.495082814
## 74 Alive -1.868775707 0.569029628 0.581800057 -1.084485611
## 75 Alive 0.683905846 1.767290796 0.241693051 -1.337566812
## 76 Alive 0.821006546 -1.188104492 0.917466077 -1.089980478
## 77 Alive -0.499967072 -0.063567628 -0.217092609 -1.242667319
## 78 Alive 0.056071716 -1.653376800 1.664161542 0.435774870
## 79 Alive 0.099588612 -1.161140621 0.358003056 -0.058098223
## 80 Alive -1.638985742 0.150875793 -1.403816856 -0.700686152
## 81 Alive 0.865297254 1.214733944 1.463461173 -0.297882350
## 82 Alive -1.545124764 0.127252910 -0.935729044 -0.793110208
## 83 Alive -0.757282603 -0.365269832 -0.559376514 -1.125365040
## 84 Alive -1.494668798 -0.862217669 -1.017557513 0.729371690
## 85 Alive -1.198962297 0.090483632 -0.244225721 0.803338834
## 86 Alive 1.053228198 0.023027292 0.260206980 0.703883631
## 87 Alive 2.839883593 -2.296312935 0.510353279 -0.693661524
## 88 Alive 1.506058603 -1.812772768 0.528733408 -0.767001468
## 89 Alive -1.539415867 -0.136768478 0.768955037 -0.049503375
## 90 Alive -2.166532837 0.071753733 0.343483494 -0.898166612
## 91 Dead 0.893002750 -1.772886261 0.734063638 -0.797845672
## 92 Alive -0.677904182 -0.104397875 0.169469929 2.673756815
## 93 Dead -0.646604416 -0.740495104 0.063231982 -1.095809541
## 94 Dead 1.683330979 1.567742424 -0.698706197 1.431672587
## 95 Alive -1.509921397 0.297490480 0.490010821 -0.323083740
## 96 Alive -0.135237286 0.293266912 -1.015571227 -0.225694168
## 97 Dead 0.027644129 -1.133291443 -1.997458759 1.032137750
## 98 Alive -0.637273583 -0.513850978 -0.306967375 -0.684532247
## 99 Dead 1.070049729 -2.036508976 -0.316339810 -0.094341352
## 100 Alive -0.455435814 0.089328755 -1.403983913 -1.027093674
## 101 Dead 4.600390311 2.244846920 0.532264308 1.259266636
## 102 Alive -0.787145836 1.086091949 0.549806202 1.093912587
## 103 Alive 0.655142324 -1.683984928 -2.308143986 2.208715115
## 104 Dead -0.428540034 -0.840500324 -1.048098702 -0.027665882
## 105 Alive -0.110654721 -0.123171275 -0.175937919 0.338031509
## 106 Alive -0.734249607 -1.236231879 -1.090037416 -0.386975718
## 107 Dead 0.296584193 -0.577728068 -2.014640498 0.588158511
## 108 Alive -1.410702952 0.429684625 -0.958296105 -0.866024725
## 109 Alive -0.418905210 -1.232525386 1.863199813 1.081316900
## 110 Alive 0.446752555 1.508585940 -0.342268303 -0.736468382
## 111 Alive -1.134059417 0.782686222 -0.521004605 -0.152263500
## 112 Dead 1.181466882 -2.299898160 0.735344703 0.997333267
## 113 Alive 1.830654533 1.883074076 0.954309940 0.626252247
## 114 Alive 0.454774207 -0.643039459 0.237045213 0.759165544
## 115 Alive 0.864920996 -1.531113286 1.149483739 -0.984234084
## 116 Alive -0.897625868 0.218458064 -0.870977930 0.772271080
## 117 Alive 1.357865125 -1.941049776 0.946671254 -0.674767960
## 118 Alive -0.915336154 1.327339693 0.352068802 -1.370754921
## 119 Alive 0.094948933 -0.356826249 1.052712045 0.237447671
## 120 Alive -0.037442692 -0.108870167 -0.518461408 0.323952099
## 121 Alive -0.703244230 -0.760629115 0.236405707 -1.666145723
## 122 Alive 1.727474232 -1.256161661 0.911292089 0.280268540
## 123 Alive 1.839479021 0.845697621 -0.141543565 0.392072998
## 124 Alive 0.275373090 0.726740366 0.643511448 -0.752337791
## 125 Alive -0.732974709 1.225314046 -0.703247765 0.876777966
## 126 Dead -0.921856464 0.796384898 -2.658215899 0.486234753
## 127 Alive -0.151799435 -0.761905068 1.710990722 1.051731292
## 128 Alive -1.471716143 -0.654343538 -1.425218658 0.191711126
## 129 Alive -1.483838817 -0.227422742 0.005677556 0.103891666
## 130 Alive -0.899242135 0.043994478 0.476955011 1.186170494
## 131 Alive -1.358439633 0.497908624 -1.167958845 0.193782726
## 132 Alive 0.549771469 -0.569819028 0.116818203 0.221134190
## 133 Alive -1.825714544 -0.294808189 0.619015786 -0.318205481
## 134 Alive -1.466418848 -0.825197537 0.473859265 0.509772598
## 135 Dead 0.713759778 -0.436347722 -1.423945946 0.210208666
## 136 Dead 0.095641779 1.526711941 0.249630093 2.345493852
## 137 Alive -0.311491252 -0.719233132 0.764263980 0.606336637
## 138 Dead -0.482193479 0.590787139 -0.436621861 -0.920884510
## 139 Dead 1.024336162 0.440548826 -0.998470261 -0.555076086
## 140 Alive 2.074951928 -0.323134611 1.585536035 -0.925846944
## 141 Alive -1.891283328 -0.671701731 0.262065322 0.249157996
## 142 Alive -0.768896963 -0.184566117 1.838693762 1.680165112
## 143 Alive -0.660225602 1.111821771 -0.488335117 1.229777710
## 144 Dead 0.458314079 0.872057326 -1.262688367 -0.394557457
## 145 Dead 0.202499186 0.236773800 -0.635093302 0.249780704
## 146 Alive -0.635694229 -0.225009929 1.204353392 -1.218165045
## 147 Alive -1.314850127 0.558262177 1.185628313 0.999319862
## 148 Dead 2.618727317 -1.043294960 -0.131770830 1.161272958
## 149 Alive -1.867933212 -0.735989177 -0.971686550 -0.761863164
## 150 Alive -0.390204192 -0.137821477 0.220960666 -0.609509106
## 151 Alive -1.169108179 0.192370763 1.849895119 1.591382674
## 152 Alive -0.593384345 0.170296655 -0.789961437 -1.081723093
## 153 Dead -1.153893444 0.470099262 -0.943547532 0.043877107
## 154 Alive -1.299586961 0.646325766 0.756131408 -0.633505535
## 155 Alive -1.312753509 0.646956638 -1.191403488 -0.628395922
## 156 Alive 2.158951805 -0.669181055 0.329330268 -2.652868558
## 157 Alive -0.888545794 0.212970263 -0.609333802 1.384522112
## 158 Alive -1.604599290 -0.895420185 1.536550848 1.466041850
## 159 Alive -0.695240701 -1.437349712 -0.294419793 0.105308219
## 160 Dead 1.698058938 0.861942358 -2.379230129 0.682957573
## 161 Alive 0.523091631 0.622823965 -2.532738018 0.414152379
## 162 Alive -1.639464234 -0.668476601 -1.067754195 0.831399161
## 163 Alive -1.775434759 -0.854401433 -0.150230446 -0.275686146
## 164 Alive -1.300191877 0.924773079 0.692943522 -0.083020548
## 165 Alive 0.127243391 0.547570383 -0.822898988 -0.399221133
## 166 Alive 0.728909729 -1.777883731 -1.474530685 -1.729305188
## 167 Alive -0.691130861 0.504125474 -0.083355531 0.385479113
## 168 Alive 4.057107584 0.177251126 2.338537102 0.287960419
## 169 Alive 0.065928057 -1.066260062 -0.766093466 0.786318654
## 170 Alive -1.537449988 0.126535183 1.129984140 0.112397316
## 171 Dead 0.005212931 0.571207430 -0.800002711 -1.395337324
## 172 Alive 1.307010016 -1.130265555 -0.298412422 -1.569287554
## 173 Alive -1.400091197 -0.281929928 0.503682489 0.734624858
## 174 Alive -1.914378275 -0.015175249 0.090929135 -0.639031301
## 175 Alive -1.354059138 1.369758171 0.970119313 -0.448346287
## 176 Alive 1.278137221 -1.653045958 0.582176145 0.663913439
## 177 Dead -0.240072950 1.468050171 -1.146791696 0.313983803
## 178 Alive -1.192542565 -0.620681157 0.393013804 1.386142742
## 179 Alive 1.517499402 2.446494185 -0.097915083 0.552779780
## 180 Dead 0.419667049 -0.327707583 -0.647757875 -0.752472503
## 181 Alive -1.183491054 2.047841110 1.056237863 -0.386605606
## 182 Dead -0.049231716 0.736575008 0.077583188 -0.705296875
## 183 Dead -1.497163756 -0.391927377 -2.671606811 0.257351508
## 184 Alive 1.362728567 0.566668154 -0.177208297 0.688607859
## 185 Alive 3.022520941 -0.826120544 0.734638502 -0.813207184
## 186 Alive -0.646848816 0.019961075 0.140097904 -1.345604301
## 187 Alive 0.841699831 -1.772549530 -0.373832896 -2.173967292
## 188 Alive -0.341629561 -0.113562351 -0.165011337 -0.351171147
## 189 Dead 0.597265999 2.425823378 1.007898127 -0.923443496
## 190 Alive -1.161264597 0.015537197 0.541717900 1.081599330
## 191 Alive -0.477014120 -0.313853416 -0.666580443 -0.171072190
## 192 Alive -2.115125949 -0.729760082 0.102680575 -0.379831150
## 193 Alive -0.991130507 1.160119732 -0.454562005 -0.255797516
## 194 Alive -0.707735717 -1.202340369 0.313311997 -0.079193489
## 195 Alive 3.115036491 -0.278203347 -0.068038843 0.730365425
## 196 Alive -1.696392904 -0.279442921 -1.520016658 -0.119474656
## 197 Alive 0.151090645 -0.052353299 -0.654184084 0.093232715
## 198 Alive 1.330786502 -1.333832490 1.198984292 -0.592071242
## 199 Alive 0.296675856 0.507260694 -0.459773048 0.471858283
## 200 Alive -0.422623151 -0.772830338 1.475442657 0.229622630
## 201 Alive -0.318075869 -0.206265532 0.193138644 -0.150273909
## 202 Alive -0.085308348 0.324848824 -0.506897761 -0.413457726
## 203 Dead -1.822877611 -0.578840959 -1.943795566 -0.354374768
## 204 Dead 1.201683038 1.016703999 -1.617844139 1.145915109
## 205 Alive -1.807181645 -0.673704761 -0.909165251 -0.542600144
## 206 Alive -1.784093888 -0.101950630 -1.523967142 -0.547484916
## 207 Alive -0.078106596 0.540840034 0.980990841 -0.492489469
## 208 Alive -0.721328123 0.145142743 1.245670834 -1.005611527
## 209 Alive -0.483839459 -0.454229646 0.058240719 -0.240884895
## 210 Alive 0.663630444 -2.030515942 1.095559877 -0.315653418
## 211 Alive 1.978468906 -1.541564858 0.344229726 0.254916972
## 212 Dead 2.937647970 0.023153745 -1.467099553 2.004769891
## 213 Alive -0.086636710 1.891839624 1.573096232 0.223299508
## 214 Alive -1.481813930 0.006331169 -1.173928063 -0.250137785
## 215 Alive 0.623006822 -0.037759847 -0.710766534 0.184537311
## 216 Dead 1.991882118 -1.666919941 -2.805934883 -0.871488718
## 217 Dead 0.744165906 -0.860059687 -1.328696095 1.365529752
## 218 Alive 0.641119818 -0.445632455 0.162013092 -2.055341520
## 219 Alive -1.586401627 -0.388025617 -1.097489991 -0.453696582
## 220 Dead 4.773395918 2.278577670 -1.336404778 0.510730406
## 221 Dead 2.921320323 -0.012042086 -1.874368061 -0.045263697
## 222 Dead 0.503935335 1.035837075 -1.154051231 -0.866417161
## 223 Alive -1.241990069 0.411074638 1.790709487 0.707551103
## 224 Alive -0.133856941 -0.846749537 0.481837944 1.031203316
## 225 Alive -1.486223026 -1.226757723 0.663500601 1.212738370
## 226 Alive -0.762041381 1.164340422 1.896521625 1.074683686
## 227 Alive 2.005021660 0.341436716 -0.409217808 -0.832010193
## 228 Alive 1.814305601 1.684900471 0.545885187 -0.444700098
## 229 Alive -1.411373860 -0.029800132 -1.219717248 -0.012627251
## 230 Alive -0.324175998 0.181346052 0.453617491 -1.500433205
## 231 Alive -0.456860329 0.176546846 0.852740264 -0.298237857
## 232 Alive -1.210396528 0.443593233 -1.157566359 -0.418875718
## 233 Alive 0.367888943 1.034558583 -0.899804344 -1.320083756
## 234 Alive -1.737267642 -0.768492804 -0.717586622 -0.042347936
## 235 Alive -1.509987525 0.519084836 0.532663661 -0.793096619
## 236 Alive -1.290446225 1.701929130 -0.262965485 -0.898972118
## 237 Alive 3.655612544 1.679581237 -0.078271387 0.366568656
## 238 Alive 0.611276361 -1.193837776 1.025840807 -1.693775105
## 239 Dead 6.711875034 1.215508748 -1.279625142 0.587766000
## 240 Alive -1.281390399 -0.456797389 0.383696463 1.327109609
## 241 Dead 0.776720455 0.873249312 -0.255587193 0.950034593
## 242 Alive 0.008347450 1.173046306 1.625650682 -0.126758712
## 243 Alive -0.958826089 -0.492058288 0.745646701 -1.985299776
## 244 Alive 1.609087788 0.768291741 1.106856868 1.288165361
## 245 Alive 0.543831815 -0.344117364 1.084227436 0.743018250
## 246 Alive -1.795501728 0.797766300 0.941073658 -0.948765046
## 247 Alive -2.078996209 0.034041364 0.343126833 -1.053156920
## 248 Dead 0.486998129 0.122844418 -0.822868404 1.350720580
## 249 Alive -0.821657492 -0.011924402 0.873543779 1.971662603
## 250 Alive -1.398504155 -0.243599402 0.837410828 0.477686433
## 251 Alive 0.526594325 -1.361027292 1.730491888 0.644317870
## 252 Alive 0.120809384 -1.392425032 -0.882175385 0.251835439
## 253 Alive -0.289560811 -1.753881720 0.731478923 1.008115634
## 254 Alive 2.350354264 -1.374432502 0.783487702 1.516771930
## 255 Alive 2.529945185 -0.796264796 -1.084229732 -1.768591624
## 256 Alive -0.594294620 0.606268901 0.546284310 -1.512570945
## 257 Alive -1.406577585 0.312852106 -0.020482861 0.091002001
## 258 Alive -1.651971076 -0.143369845 -1.143133022 -0.250064542
## 259 Alive 0.415871178 -0.214174686 0.915948123 0.956618386
## 260 Alive -0.286827613 -0.440600376 -0.511227621 -0.188717119
## 261 Alive -0.645411407 0.058506107 -2.305257330 2.581332331
## 262 Alive -0.628353063 -1.040695063 1.499765220 0.328717274
## 263 Alive -0.136446586 -0.912547265 0.240795333 0.609862680
## 264 Dead -1.777655604 -0.274014123 -1.028075306 -0.764011769
## 265 Alive -1.357302997 2.288698502 1.019344070 -1.133889152
## 266 Alive -1.150407815 -1.178196185 0.453312973 -1.488628969
## 267 Alive -0.854919366 2.319121839 -0.534036982 -0.401249649
## 268 Alive 1.748954057 -2.489466264 0.147763981 1.527744484
## 269 Dead -0.738423976 -0.871268532 -1.716222096 -0.549433967
## 270 Alive -0.346935263 1.923554748 -1.292856361 -0.360145431
## 271 Dead 2.611945346 -0.868543943 -0.456914061 1.833405222
## 272 Alive -0.054669716 0.467014101 -0.459580646 0.187565076
## 273 Alive 0.590763284 0.081986670 -0.821826225 1.066920091
## 274 Alive -0.771766282 0.497567733 -0.144543170 -0.043136586
## 275 Alive 0.287407340 -0.999343796 -0.141647094 1.726767706
## 276 Alive -1.904210848 -0.711924915 -0.636156799 0.229311959
## 277 Alive 1.980934953 -2.144737237 -1.558960290 -1.734660915
## 278 Dead 4.349982486 0.818990696 -1.850629065 0.156456507
## 279 Alive -1.601460087 0.466219801 0.555412046 -1.282120597
## 280 Alive 1.110817200 -0.894199685 0.626718163 -1.090577512
## 281 Alive -1.635586546 0.585764692 0.351472824 -0.436299965
## 282 Alive -0.910449829 -0.063109780 -0.243265787 1.440217859
## 283 Dead 0.979721615 0.904442368 -1.232199254 1.008144535
## 284 Alive -0.472435837 -0.521473629 0.942802823 0.140237047
## 285 Alive 0.298128461 -0.439838094 -0.230211394 0.045875504
## 286 Dead 0.876478490 -0.632485240 -2.150246922 0.523252544
## 287 Alive 0.030556752 -0.246001099 -1.050954176 -0.130320899
## 288 Alive 0.489276289 0.149716001 1.343990756 -0.776952747
## 289 Alive 1.167193218 4.324487587 0.744165112 -1.104452819
## 290 Dead 5.639123713 1.493129585 0.436631086 0.391589194
## 291 Alive 0.076038156 2.149080398 1.231684279 -0.889701456
## 292 Alive -1.306362503 0.777428880 -0.836033189 -0.505010722
## 293 Dead -1.492629535 0.346667458 -1.594060891 -0.744201427
## 294 Alive 0.548191410 0.159332266 1.521957843 0.691090269
## 295 Alive 3.173294742 -0.713640891 1.483201289 -0.597042450
## 296 Alive -1.711510331 0.207909220 -0.931632873 -0.732023246
## 297 Alive -1.420928885 -1.297938310 0.314667960 1.070874265
## 298 Alive -0.397038374 -0.140558009 -0.100049951 -1.210608408
## 299 Alive -1.338159554 0.850035604 0.991498508 0.275292019
## 300 Alive 1.238726422 -0.682019739 -1.206227105 -1.584533216
## 301 Alive 0.476798036 -0.538294379 1.306977504 0.589987890
## 302 Alive 0.451358041 0.509847268 -0.404959275 1.025191596
## 303 Alive -0.410664267 1.809811675 0.163254213 1.203959868
## 304 Alive 0.631511135 4.553878477 0.617849698 -0.258625983
## 305 Alive 0.606275351 1.307303704 -1.190130416 -1.085147986
## 306 Dead 3.760469200 -1.318016453 -1.571659239 -0.958198521
## 307 Alive 0.283257978 0.334225557 0.900109850 1.387190281
## 308 Alive 1.205872572 -1.025116718 -0.694241491 -0.489820821
## 309 Alive -0.547890175 -1.378267017 0.199506501 0.006777245
## 310 Alive 0.675442079 -0.040092847 0.040280714 1.538300103
## 311 Alive -0.347420655 -1.297275709 -0.084885546 0.216594996
## 312 Alive -1.082694803 1.058501944 -1.274637266 -0.535652316
## 313 Alive -0.809911038 0.678119879 -0.193503870 0.489931605
## 314 Dead 2.814192996 1.465015414 1.296910650 -1.024401483
## 315 Alive -1.219216145 -0.216402526 0.775638956 0.706433637
## 316 Alive -0.839858529 -1.160921154 -0.067522123 -0.376613864
## 317 Alive 1.906604890 -1.476681383 -0.028831221 0.037013607
## 318 Alive -1.128786006 0.395890021 0.040446729 0.390323605
## 319 Alive 4.980287452 1.400993226 0.386980437 0.646687478
## 320 Alive -0.396555408 -0.215395452 -1.222389233 -0.813225124
## 321 Alive -1.686147468 0.664222126 1.210799613 -0.375476795
## 322 Alive -0.771587552 0.001912498 -0.021523533 2.182231316
## 323 Alive 2.121003409 -2.080663494 0.161998088 0.897550000
## 324 Alive 0.183525269 0.711131176 0.676974276 -0.837925098
## 325 Alive -0.388480855 -0.019183155 -0.034180507 -0.379134234
## 326 Alive -0.270374270 0.372642009 0.619830911 -1.148519958
## 327 Alive -0.016309255 -0.272150173 1.123754077 -0.347941297
## 328 Alive -1.509365115 -1.227221931 0.110956778 1.437386493
## 329 Alive 1.128006246 -1.746278013 0.499382396 -1.619420542
## 330 Alive -0.013678857 0.097843119 0.408072714 -0.795855347
## 331 Alive 0.134239505 0.261168839 1.687827776 0.217195174
## 332 Dead 0.543266130 0.289044087 -1.889627887 1.415180585
## 333 Alive -1.694510184 -0.384164773 0.978956440 -0.619188118
## 334 Alive -1.177192240 0.755347480 -0.072837954 0.262273753
## 335 Alive -0.154704801 -0.482019591 -0.130393501 0.108703255
## 336 Alive -1.222393212 -0.140605864 0.470903440 0.854635087
## 337 Alive 0.985284375 -2.085350193 -0.309169317 -0.356636930
## 338 Alive 1.845084419 -1.284127961 -0.428328294 -1.460289251
## 339 Alive -1.537001279 1.111570387 0.652894920 -1.060718845
## 340 Alive 0.486580696 -0.438599188 -0.143918334 0.966749788
## 341 Alive -0.381846642 -0.365594889 0.626052636 0.039508221
## 342 Alive -1.058469609 1.839970213 -0.254329772 -0.731552164
## 343 Alive 1.953784231 -1.229071105 0.160259672 0.867246394
## 344 Alive -1.632770525 -0.310017947 0.586575867 0.624972262
## 345 Alive -0.069211481 1.179578849 -0.019456868 -1.025693279
## 346 Alive 0.924645953 0.318200997 -0.038558980 -0.176342543
## 347 Alive -1.679627649 -0.870249748 1.201962925 0.638583744
## 348 Alive -0.138978457 -0.327879510 1.445999742 0.018109114
## 349 Alive -0.306354427 2.443421548 0.256738595 0.723881262
## 350 Alive -1.082397105 0.511694553 0.396630701 0.376171916
## 351 Alive 1.560087096 -0.172608049 2.042673531 0.001387343
## 352 Alive 0.213890453 0.121650120 -0.363220480 0.143134581
## 353 Alive -1.243101129 -0.469575151 -1.404226113 1.148855158
## 354 Alive -1.723673624 -0.628891973 1.215101216 0.822337346
## 355 Alive -1.845736715 -1.246640827 1.218806001 0.592440275
## 356 Alive -0.533908899 0.509703545 -1.010222476 -1.067833304
## 357 Alive -0.621852817 1.060330174 -0.185420284 0.974853637
## 358 Dead -0.663822556 -0.698693563 -1.437208451 -1.000964685
## 359 Alive -1.464448793 -0.997923794 0.090438438 0.991886193
## 360 Alive -1.523194528 1.088366756 -0.015584201 -1.071387626
## 361 Alive -0.249284791 -0.495162923 -0.888175969 0.194375075
## 362 Alive -0.978278825 0.745196276 1.673492426 0.624652999
## 363 Dead 2.298810986 -0.090143085 -0.751106742 -0.561856912
## 364 Dead -0.641761160 -1.573225212 0.960424847 -0.179437036
## 365 Alive -1.237501132 -0.412442737 1.793811573 1.137104529
## 366 Alive -1.157403928 0.923508573 -0.442026074 -0.884941552
## 367 Alive -0.796933393 1.222876039 0.723404723 -0.237384378
## 368 Alive 2.646899548 0.301553970 0.690593527 -2.443750630
## 369 Alive -0.178975454 -0.138624086 1.105283992 -1.499072183
## 370 Dead -1.330874437 0.769296425 -0.127097036 -1.223980155
## 371 Alive 0.785519987 2.132318925 0.981263612 -0.639682484
## 372 Dead 4.528600634 -0.995996130 0.568209680 -0.292649916
## 373 Alive -2.215387412 -0.717213408 0.437807288 -1.098624561
## 374 Alive 0.852816653 0.697424945 -0.415247520 0.859928559
## 375 Alive 1.528575274 1.579100810 0.424898608 1.740887715
## 376 Alive 1.052831636 0.469776583 0.746395631 -0.477473960
## 377 Alive 3.308075529 -0.637217047 -0.361014725 -0.281269186
## 378 Alive 0.145308323 -0.337470348 1.183817291 1.285154406
## 379 Alive -0.100434292 -0.148112235 0.886936726 0.259148546
## PC5 PC6
## 1 0.852277723 0.116709537
## 2 -0.014925567 0.110173000
## 3 -0.039058417 0.151011377
## 4 -0.771910136 -0.343807479
## 5 -0.078371793 -0.068417317
## 6 0.233248754 -0.420280958
## 7 0.038121315 0.014839886
## 8 0.548288673 0.336718257
## 9 -0.724303190 -0.045952454
## 10 -0.376692694 1.939826284
## 11 -0.204199065 -0.146897222
## 12 0.266696937 0.183314250
## 13 0.200775716 0.114162471
## 14 0.141353261 -0.102727402
## 15 -1.296448032 0.196911289
## 16 0.742413832 -0.296960713
## 17 -0.578346113 -0.346683316
## 18 1.134795943 0.385229903
## 19 0.402986436 0.250212417
## 20 0.860603335 0.210997273
## 21 0.372107468 0.178758339
## 22 0.135596833 -0.003801151
## 23 -0.280109421 0.217319459
## 24 1.064729564 -0.187966712
## 25 -2.330312186 -0.249408299
## 26 -0.785747318 0.582504343
## 27 -2.125689786 -0.264956027
## 28 0.143564512 -0.324073726
## 29 0.043817854 0.392690074
## 30 0.016907630 0.433561922
## 31 -0.096628489 -0.044052794
## 32 -0.330970546 -0.172924722
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## 34 0.292432820 -0.339264995
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## 37 0.437914429 0.414287669
## 38 -0.155155562 -0.393701821
## 39 0.029439452 0.033505637
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## 49 -0.634281043 0.187074835
## 50 -0.742921582 0.063584865
## 51 0.429398197 0.411945392
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## 53 0.605914036 -1.602200768
## 54 1.244480037 -0.297652746
## 55 0.215871580 0.140534670
## 56 0.063005452 -0.120117267
## 57 0.669994233 0.295188323
## 58 2.502769179 -0.436240290
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## 318 -0.149885563 -0.221941061
## 319 -1.083846603 -0.754255469
## 320 0.424557329 0.249838558
## 321 0.198108774 -0.111526776
## 322 0.393142757 -0.207650126
## 323 0.380306029 -0.362767449
## 324 -0.201495035 0.207891984
## 325 0.583222451 0.340268457
## 326 -0.407017698 0.368766457
## 327 -0.103237180 0.012058601
## 328 -0.758506439 -0.149559490
## 329 0.555724903 1.463155184
## 330 -1.175223096 0.382942476
## 331 1.082628063 -0.032112095
## 332 1.063577278 0.397084457
## 333 -0.943767153 -0.354911460
## 334 0.532730202 -0.233823936
## 335 0.455787032 0.146812456
## 336 -0.236602493 -0.250028422
## 337 0.209646403 0.205107833
## 338 0.838247554 -0.667916271
## 339 -0.002140100 -0.159417162
## 340 0.107166844 0.044940196
## 341 -0.092159877 0.444365443
## 342 -0.827823834 0.218371896
## 343 1.295990204 -0.083864131
## 344 -0.312659105 -0.066718642
## 345 0.424192027 0.460637350
## 346 -1.278270521 0.010040209
## 347 -0.657934688 -0.249703684
## 348 0.324021275 0.069849151
## 349 0.004780055 0.133553509
## 350 0.200267508 -0.337335972
## 351 0.943307040 0.358285729
## 352 0.251009799 0.221064477
## 353 -0.206147146 -0.125296735
## 354 -0.530509884 -0.070458295
## 355 -0.970712299 -0.224997131
## 356 0.770760459 0.501370980
## 357 0.788314716 -0.349367892
## 358 -0.267520648 0.380452253
## 359 -0.619748924 -0.271394600
## 360 0.484479318 -0.258419685
## 361 0.137323234 0.402658885
## 362 0.677279063 -0.468027915
## 363 1.569191798 -0.324990632
## 364 -0.696431558 0.142034987
## 365 -0.371283677 -0.347928412
## 366 -0.171459484 -0.351391164
## 367 -0.510118334 -0.285977778
## 368 0.663805037 -0.971457197
## 369 -0.164055484 -0.181523245
## 370 -0.869663470 -0.240725882
## 371 -0.035075161 0.387573331
## 372 -0.397415282 -0.229079837
## 373 -0.945243579 -0.209054420
## 374 0.964247801 0.036780440
## 375 -0.368739736 0.503922523
## 376 -1.373515237 -0.173505314
## 377 -0.462933899 -0.787406645
## 378 0.271835930 0.319960047
## 379 0.704812541 0.154968029
# Means of scores for all the PC's classified by Survival status
tabmeansPC <- aggregate(sparrtyp_pca[,2:6],by=list(Survivor=Cancer$Survivor),mean)
tabmeansPC
## Survivor PC1 PC2 PC3 PC4 PC5
## 1 Alive -0.1900732 -0.02921761 0.1740706 -0.03610293 0.01331074
## 2 Dead 1.0309052 0.15846840 -0.9441118 0.19581249 -0.07219385
tabmeansPC <- tabmeansPC[rev(order(tabmeansPC$Survivor)),]
tabmeansPC
## Survivor PC1 PC2 PC3 PC4 PC5
## 2 Dead 1.0309052 0.15846840 -0.9441118 0.19581249 -0.07219385
## 1 Alive -0.1900732 -0.02921761 0.1740706 -0.03610293 0.01331074
tabfmeans <- t(tabmeansPC[,-1])
tabfmeans
## 2 1
## PC1 1.03090525 -0.19007315
## PC2 0.15846840 -0.02921761
## PC3 -0.94411177 0.17407061
## PC4 0.19581249 -0.03610293
## PC5 -0.07219385 0.01331074
colnames(tabfmeans) <- t(as.vector(tabmeansPC[1]$Survivor))
tabfmeans
## Dead Alive
## PC1 1.03090525 -0.19007315
## PC2 0.15846840 -0.02921761
## PC3 -0.94411177 0.17407061
## PC4 0.19581249 -0.03610293
## PC5 -0.07219385 0.01331074
# Standard deviations of scores for all the PC's classified by Survival status
tabsdsPC <- aggregate(sparrtyp_pca[,2:6],by=list(Survivor=Cancer$Survivor),sd)
tabfsds <- t(tabsdsPC[,-1])
colnames(tabfsds) <- t(as.vector(tabsdsPC[1]$Survivor))
tabfsds
## Alive Dead
## PC1 1.3032441 1.9907117
## PC2 1.0674058 1.1383653
## PC3 0.8852042 0.9965457
## PC4 0.9481136 1.0060030
## PC5 0.7030204 0.7743521
t.test(PC1~Cancer$Survivor,data=sparrtyp_pca)
##
## Welch Two Sample t-test
##
## data: PC1 by Cancer$Survivor
## t = -4.5354, df = 67.452, p-value = 2.424e-05
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
## -1.7582650 -0.6836918
## sample estimates:
## mean in group Alive mean in group Dead
## -0.1900732 1.0309052
t.test(PC2~Cancer$Survivor,data=sparrtyp_pca)
##
## Welch Two Sample t-test
##
## data: PC2 by Cancer$Survivor
## t = -1.1748, df = 77.956, p-value = 0.2437
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
## -0.5057542 0.1303822
## sample estimates:
## mean in group Alive mean in group Dead
## -0.02921761 0.15846840
t.test(PC3~Cancer$Survivor,data=sparrtyp_pca)
##
## Welch Two Sample t-test
##
## data: PC3 by Cancer$Survivor
## t = 8.0528, df = 75.811, p-value = 8.857e-12
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
## 0.8416157 1.3947491
## sample estimates:
## mean in group Alive mean in group Dead
## 0.1740706 -0.9441118
t.test(PC4~Cancer$Survivor,data=sparrtyp_pca)
##
## Welch Two Sample t-test
##
## data: PC4 by Cancer$Survivor
## t = -1.6414, df = 78.171, p-value = 0.1047
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
## -0.51318907 0.04935823
## sample estimates:
## mean in group Alive mean in group Dead
## -0.03610293 0.19581249
t.test(PC5~Cancer$Survivor,data=sparrtyp_pca)
##
## Welch Two Sample t-test
##
## data: PC5 by Cancer$Survivor
## t = 0.79023, df = 76.646, p-value = 0.4318
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
## -0.1299680 0.3009772
## sample estimates:
## mean in group Alive mean in group Dead
## 0.01331074 -0.07219385
## F ratio tests
var.test(PC1~Cancer$Survivor,data=sparrtyp_pca)
##
## F test to compare two variances
##
## data: PC1 by Cancer$Survivor
## F = 0.42858, num df = 319, denom df = 58, p-value = 3.45e-06
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
## 0.2797709 0.6211181
## sample estimates:
## ratio of variances
## 0.4285828
var.test(PC2~Cancer$Survivor,data=sparrtyp_pca)
##
## F test to compare two variances
##
## data: PC2 by Cancer$Survivor
## F = 0.87922, num df = 319, denom df = 58, p-value = 0.4886
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
## 0.5739361 1.2741931
## sample estimates:
## ratio of variances
## 0.8792165
var.test(PC3~Cancer$Survivor,data=sparrtyp_pca)
##
## F test to compare two variances
##
## data: PC3 by Cancer$Survivor
## F = 0.78903, num df = 319, denom df = 58, p-value = 0.2112
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
## 0.5150629 1.1434889
## sample estimates:
## ratio of variances
## 0.7890282
var.test(PC4~Cancer$Survivor,data=sparrtyp_pca)
##
## F test to compare two variances
##
## data: PC4 by Cancer$Survivor
## F = 0.88822, num df = 319, denom df = 58, p-value = 0.5217
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
## 0.5798156 1.2872462
## sample estimates:
## ratio of variances
## 0.8882233
var.test(PC5~Cancer$Survivor,data=sparrtyp_pca)
##
## F test to compare two variances
##
## data: PC5 by Cancer$Survivor
## F = 0.82425, num df = 319, denom df = 58, p-value = 0.306
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
## 0.538055 1.194534
## sample estimates:
## ratio of variances
## 0.8242499
# Levene's tests (one-sided)
library(car)
## Loading required package: carData
##
## Attaching package: 'car'
##
## The following object is masked from 'package:purrr':
##
## some
##
## The following object is masked from 'package:dplyr':
##
## recode
(LTPC1 <- leveneTest(PC1~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 1 13.574 0.0002629 ***
## 377
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(p_PC1_1sided <- LTPC1[[3]][1]/2)
## [1] 0.0001314606
(LTPC2 <- leveneTest(PC2~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 1 1.8085 0.1795
## 377
(p_PC2_1sided=LTPC2[[3]][1]/2)
## [1] 0.08975099
(LTPC3 <- leveneTest(PC3~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 1 0.8964 0.3444
## 377
(p_PC3_1sided <- LTPC3[[3]][1]/2)
## [1] 0.1721817
(LTPC4 <- leveneTest(PC4~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 1 0.958 0.3283
## 377
(p_PC4_1sided <- LTPC4[[3]][1]/2)
## [1] 0.1641622
(LTPC5 <- leveneTest(PC5~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 1 1.7506 0.1866
## 377
(p_PC5_1sided <- LTPC5[[3]][1]/2)
## [1] 0.09330252
# Plotting the scores for the first and second components
plot(sparrtyp_pca$PC1, sparrtyp_pca$PC2,pch=ifelse(sparrtyp_pca$Survivor == "S",1,16),xlab="PC1", ylab="PC2", main="49 sparrows against values for PC1 & PC2")
abline(h=0)
abline(v=0)
legend("bottomleft", legend=c("Survivor","Nonsurvivor"), pch=c(1,16))
plot(eigen_Cancer, xlab = "Component number", ylab = "Component variance", type = "l", main = "Scree diagram")
plot(log(eigen_Cancer), xlab = "Component number",ylab = "log(Component variance)", type="l",main = "Log(eigenvalue) diagram")
print(summary(Cancer_pca))
## Importance of components:
## PC1 PC2 PC3 PC4 PC5 PC6
## Standard deviation 1.496 1.0794 0.9892 0.9597 0.71419 0.43317
## Proportion of Variance 0.373 0.1942 0.1631 0.1535 0.08501 0.03127
## Cumulative Proportion 0.373 0.5672 0.7302 0.8837 0.96873 1.00000
diag(cov(Cancer_pca$x))
## PC1 PC2 PC3 PC4 PC5 PC6
## 2.2378787 1.1649997 0.9784385 0.9209868 0.5100636 0.1876326
xlim <- range(Cancer_pca$x[,1])
Cancer_pca$x[,1]
## [1] -1.493744354 0.426322428 1.694207768 -1.767583528 0.043714825
## [6] -1.028534021 -1.338771984 0.406514411 4.993025728 1.937948477
## [11] -1.756901401 1.296312778 -0.090142691 -0.076244034 1.004107956
## [16] -1.005634503 -0.538374841 0.204445317 -0.419443766 -0.252782392
## [21] -0.036353656 0.504291512 -0.618672209 1.459334722 0.693501261
## [26] 1.342457422 2.475721782 -1.137184838 -0.082096727 -0.951459346
## [31] 0.004306142 -1.358590305 -1.790419403 -0.908445651 1.245709794
## [36] -1.439873416 0.636390371 -1.304428696 -0.097417933 -0.188925650
## [41] 2.535953943 -1.364589888 -1.095258604 0.018958421 -1.483766860
## [46] 0.803570710 -0.776759752 -1.440160549 0.550199236 -1.959716237
## [51] 0.283946083 0.584420507 2.164109035 1.673683848 -1.630123732
## [56] -1.450559221 -0.534036352 -0.354843129 -1.178588655 -1.248535425
## [61] -0.944827480 -1.056029210 -0.473763736 1.681009012 -1.312786276
## [66] -1.639877002 4.455166578 -0.707613499 -1.710632794 -1.171903123
## [71] 3.302612150 2.121655213 0.528823585 -1.868775707 0.683905846
## [76] 0.821006546 -0.499967072 0.056071716 0.099588612 -1.638985742
## [81] 0.865297254 -1.545124764 -0.757282603 -1.494668798 -1.198962297
## [86] 1.053228198 2.839883593 1.506058603 -1.539415867 -2.166532837
## [91] 0.893002750 -0.677904182 -0.646604416 1.683330979 -1.509921397
## [96] -0.135237286 0.027644129 -0.637273583 1.070049729 -0.455435814
## [101] 4.600390311 -0.787145836 0.655142324 -0.428540034 -0.110654721
## [106] -0.734249607 0.296584193 -1.410702952 -0.418905210 0.446752555
## [111] -1.134059417 1.181466882 1.830654533 0.454774207 0.864920996
## [116] -0.897625868 1.357865125 -0.915336154 0.094948933 -0.037442692
## [121] -0.703244230 1.727474232 1.839479021 0.275373090 -0.732974709
## [126] -0.921856464 -0.151799435 -1.471716143 -1.483838817 -0.899242135
## [131] -1.358439633 0.549771469 -1.825714544 -1.466418848 0.713759778
## [136] 0.095641779 -0.311491252 -0.482193479 1.024336162 2.074951928
## [141] -1.891283328 -0.768896963 -0.660225602 0.458314079 0.202499186
## [146] -0.635694229 -1.314850127 2.618727317 -1.867933212 -0.390204192
## [151] -1.169108179 -0.593384345 -1.153893444 -1.299586961 -1.312753509
## [156] 2.158951805 -0.888545794 -1.604599290 -0.695240701 1.698058938
## [161] 0.523091631 -1.639464234 -1.775434759 -1.300191877 0.127243391
## [166] 0.728909729 -0.691130861 4.057107584 0.065928057 -1.537449988
## [171] 0.005212931 1.307010016 -1.400091197 -1.914378275 -1.354059138
## [176] 1.278137221 -0.240072950 -1.192542565 1.517499402 0.419667049
## [181] -1.183491054 -0.049231716 -1.497163756 1.362728567 3.022520941
## [186] -0.646848816 0.841699831 -0.341629561 0.597265999 -1.161264597
## [191] -0.477014120 -2.115125949 -0.991130507 -0.707735717 3.115036491
## [196] -1.696392904 0.151090645 1.330786502 0.296675856 -0.422623151
## [201] -0.318075869 -0.085308348 -1.822877611 1.201683038 -1.807181645
## [206] -1.784093888 -0.078106596 -0.721328123 -0.483839459 0.663630444
## [211] 1.978468906 2.937647970 -0.086636710 -1.481813930 0.623006822
## [216] 1.991882118 0.744165906 0.641119818 -1.586401627 4.773395918
## [221] 2.921320323 0.503935335 -1.241990069 -0.133856941 -1.486223026
## [226] -0.762041381 2.005021660 1.814305601 -1.411373860 -0.324175998
## [231] -0.456860329 -1.210396528 0.367888943 -1.737267642 -1.509987525
## [236] -1.290446225 3.655612544 0.611276361 6.711875034 -1.281390399
## [241] 0.776720455 0.008347450 -0.958826089 1.609087788 0.543831815
## [246] -1.795501728 -2.078996209 0.486998129 -0.821657492 -1.398504155
## [251] 0.526594325 0.120809384 -0.289560811 2.350354264 2.529945185
## [256] -0.594294620 -1.406577585 -1.651971076 0.415871178 -0.286827613
## [261] -0.645411407 -0.628353063 -0.136446586 -1.777655604 -1.357302997
## [266] -1.150407815 -0.854919366 1.748954057 -0.738423976 -0.346935263
## [271] 2.611945346 -0.054669716 0.590763284 -0.771766282 0.287407340
## [276] -1.904210848 1.980934953 4.349982486 -1.601460087 1.110817200
## [281] -1.635586546 -0.910449829 0.979721615 -0.472435837 0.298128461
## [286] 0.876478490 0.030556752 0.489276289 1.167193218 5.639123713
## [291] 0.076038156 -1.306362503 -1.492629535 0.548191410 3.173294742
## [296] -1.711510331 -1.420928885 -0.397038374 -1.338159554 1.238726422
## [301] 0.476798036 0.451358041 -0.410664267 0.631511135 0.606275351
## [306] 3.760469200 0.283257978 1.205872572 -0.547890175 0.675442079
## [311] -0.347420655 -1.082694803 -0.809911038 2.814192996 -1.219216145
## [316] -0.839858529 1.906604890 -1.128786006 4.980287452 -0.396555408
## [321] -1.686147468 -0.771587552 2.121003409 0.183525269 -0.388480855
## [326] -0.270374270 -0.016309255 -1.509365115 1.128006246 -0.013678857
## [331] 0.134239505 0.543266130 -1.694510184 -1.177192240 -0.154704801
## [336] -1.222393212 0.985284375 1.845084419 -1.537001279 0.486580696
## [341] -0.381846642 -1.058469609 1.953784231 -1.632770525 -0.069211481
## [346] 0.924645953 -1.679627649 -0.138978457 -0.306354427 -1.082397105
## [351] 1.560087096 0.213890453 -1.243101129 -1.723673624 -1.845736715
## [356] -0.533908899 -0.621852817 -0.663822556 -1.464448793 -1.523194528
## [361] -0.249284791 -0.978278825 2.298810986 -0.641761160 -1.237501132
## [366] -1.157403928 -0.796933393 2.646899548 -0.178975454 -1.330874437
## [371] 0.785519987 4.528600634 -2.215387412 0.852816653 1.528575274
## [376] 1.052831636 3.308075529 0.145308323 -0.100434292
Cancer_pca$x
## PC1 PC2 PC3 PC4 PC5
## [1,] -1.493744354 1.672703734 -0.797771118 -0.639380539 0.852277723
## [2,] 0.426322428 -0.124086338 -0.222112841 0.478038848 -0.014925567
## [3,] 1.694207768 -0.545124348 0.069937198 -1.032701826 -0.039058417
## [4,] -1.767583528 -0.885302494 -0.030847119 -0.208720400 -0.771910136
## [5,] 0.043714825 -1.603388200 -0.903121553 0.849669634 -0.078371793
## [6,] -1.028534021 0.502739380 0.863904840 0.421284750 0.233248754
## [7,] -1.338771984 0.023023987 -0.740136022 1.021953281 0.038121315
## [8,] 0.406514411 -0.944219552 -1.935001240 2.169992691 0.548288673
## [9,] 4.993025728 -0.305103355 0.801778453 0.176933443 -0.724303190
## [10,] 1.937948477 0.689507346 0.639790414 -2.348269489 -0.376692694
## [11,] -1.756901401 0.140915113 -1.036789014 -0.816405788 -0.204199065
## [12,] 1.296312778 -1.473829054 1.127778467 -0.112920985 0.266696937
## [13,] -0.090142691 -0.016296775 -1.070302648 -0.891412586 0.200775716
## [14,] -0.076244034 1.581531699 -0.943407970 1.540387096 0.141353261
## [15,] 1.004107956 1.120512340 -0.515080564 -0.672554789 -1.296448032
## [16,] -1.005634503 0.998331229 -1.092830786 0.057925043 0.742413832
## [17,] -0.538374841 -1.839056096 0.934166263 -0.882076640 -0.578346113
## [18,] 0.204445317 0.244548369 0.249012257 1.256474649 1.134795943
## [19,] -0.419443766 -0.379535399 1.728764442 0.083365143 0.402986436
## [20,] -0.252782392 0.344103196 0.155613436 -0.655869450 0.860603335
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## [85,] -1.198962297 0.090483632 -0.244225721 0.803338834 0.150630291
## [86,] 1.053228198 0.023027292 0.260206980 0.703883631 -1.086933498
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## [92,] -0.677904182 -0.104397875 0.169469929 2.673756815 0.405882517
## [93,] -0.646604416 -0.740495104 0.063231982 -1.095809541 -0.767513218
## [94,] 1.683330979 1.567742424 -0.698706197 1.431672587 -1.080548515
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## [101,] 4.600390311 2.244846920 0.532264308 1.259266636 -1.010942778
## [102,] -0.787145836 1.086091949 0.549806202 1.093912587 0.984179992
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## [110,] 0.446752555 1.508585940 -0.342268303 -0.736468382 1.406332814
## [111,] -1.134059417 0.782686222 -0.521004605 -0.152263500 -0.210024740
## [112,] 1.181466882 -2.299898160 0.735344703 0.997333267 -0.237945040
## [113,] 1.830654533 1.883074076 0.954309940 0.626252247 0.685943765
## [114,] 0.454774207 -0.643039459 0.237045213 0.759165544 0.470129822
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## [116,] -0.897625868 0.218458064 -0.870977930 0.772271080 -0.128040261
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## [119,] 0.094948933 -0.356826249 1.052712045 0.237447671 0.183785081
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## [122,] 1.727474232 -1.256161661 0.911292089 0.280268540 0.754418800
## [123,] 1.839479021 0.845697621 -0.141543565 0.392072998 -1.461521820
## [124,] 0.275373090 0.726740366 0.643511448 -0.752337791 0.616212060
## [125,] -0.732974709 1.225314046 -0.703247765 0.876777966 0.813571603
## [126,] -0.921856464 0.796384898 -2.658215899 0.486234753 0.662707828
## [127,] -0.151799435 -0.761905068 1.710990722 1.051731292 0.112226358
## [128,] -1.471716143 -0.654343538 -1.425218658 0.191711126 -0.481284081
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## [131,] -1.358439633 0.497908624 -1.167958845 0.193782726 0.263406749
## [132,] 0.549771469 -0.569819028 0.116818203 0.221134190 -0.470229839
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## [137,] -0.311491252 -0.719233132 0.764263980 0.606336637 0.268751238
## [138,] -0.482193479 0.590787139 -0.436621861 -0.920884510 0.862037778
## [139,] 1.024336162 0.440548826 -0.998470261 -0.555076086 -0.681175727
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## [142,] -0.768896963 -0.184566117 1.838693762 1.680165112 -0.464801156
## [143,] -0.660225602 1.111821771 -0.488335117 1.229777710 1.056964399
## [144,] 0.458314079 0.872057326 -1.262688367 -0.394557457 1.037856081
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## [147,] -1.314850127 0.558262177 1.185628313 0.999319862 0.144248090
## [148,] 2.618727317 -1.043294960 -0.131770830 1.161272958 0.005960761
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## [151,] -1.169108179 0.192370763 1.849895119 1.591382674 0.295730175
## [152,] -0.593384345 0.170296655 -0.789961437 -1.081723093 0.289525424
## [153,] -1.153893444 0.470099262 -0.943547532 0.043877107 0.353141392
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## [155,] -1.312753509 0.646956638 -1.191403488 -0.628395922 0.086051165
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## [157,] -0.888545794 0.212970263 -0.609333802 1.384522112 0.409559425
## [158,] -1.604599290 -0.895420185 1.536550848 1.466041850 -0.589748801
## [159,] -0.695240701 -1.437349712 -0.294419793 0.105308219 -0.399801541
## [160,] 1.698058938 0.861942358 -2.379230129 0.682957573 -1.045815512
## [161,] 0.523091631 0.622823965 -2.532738018 0.414152379 0.690049934
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## [165,] 0.127243391 0.547570383 -0.822898988 -0.399221133 -0.079945323
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## [167,] -0.691130861 0.504125474 -0.083355531 0.385479113 -0.862138722
## [168,] 4.057107584 0.177251126 2.338537102 0.287960419 -0.658831067
## [169,] 0.065928057 -1.066260062 -0.766093466 0.786318654 0.249756112
## [170,] -1.537449988 0.126535183 1.129984140 0.112397316 -0.018753320
## [171,] 0.005212931 0.571207430 -0.800002711 -1.395337324 0.831843303
## [172,] 1.307010016 -1.130265555 -0.298412422 -1.569287554 0.386355543
## [173,] -1.400091197 -0.281929928 0.503682489 0.734624858 -0.419971994
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## [175,] -1.354059138 1.369758171 0.970119313 -0.448346287 0.532923665
## [176,] 1.278137221 -1.653045958 0.582176145 0.663913439 0.681887219
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## [178,] -1.192542565 -0.620681157 0.393013804 1.386142742 -0.481003615
## [179,] 1.517499402 2.446494185 -0.097915083 0.552779780 -0.177111692
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## [181,] -1.183491054 2.047841110 1.056237863 -0.386605606 1.280456900
## [182,] -0.049231716 0.736575008 0.077583188 -0.705296875 0.945577855
## [183,] -1.497163756 -0.391927377 -2.671606811 0.257351508 -0.356818941
## [184,] 1.362728567 0.566668154 -0.177208297 0.688607859 -1.112237695
## [185,] 3.022520941 -0.826120544 0.734638502 -0.813207184 -0.481935310
## [186,] -0.646848816 0.019961075 0.140097904 -1.345604301 0.174968361
## [187,] 0.841699831 -1.772549530 -0.373832896 -2.173967292 -0.270196135
## [188,] -0.341629561 -0.113562351 -0.165011337 -0.351171147 0.299781146
## [189,] 0.597265999 2.425823378 1.007898127 -0.923443496 0.528966635
## [190,] -1.161264597 0.015537197 0.541717900 1.081599330 0.151672237
## [191,] -0.477014120 -0.313853416 -0.666580443 -0.171072190 0.361420355
## [192,] -2.115125949 -0.729760082 0.102680575 -0.379831150 -0.871667253
## [193,] -0.991130507 1.160119732 -0.454562005 -0.255797516 0.085487828
## [194,] -0.707735717 -1.202340369 0.313311997 -0.079193489 -0.266559479
## [195,] 3.115036491 -0.278203347 -0.068038843 0.730365425 -0.555712164
## [196,] -1.696392904 -0.279442921 -1.520016658 -0.119474656 -0.395871345
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## [198,] 1.330786502 -1.333832490 1.198984292 -0.592071242 -0.156910522
## [199,] 0.296675856 0.507260694 -0.459773048 0.471858283 1.040250209
## [200,] -0.422623151 -0.772830338 1.475442657 0.229622630 -0.080166317
## [201,] -0.318075869 -0.206265532 0.193138644 -0.150273909 0.272483012
## [202,] -0.085308348 0.324848824 -0.506897761 -0.413457726 0.183316995
## [203,] -1.822877611 -0.578840959 -1.943795566 -0.354374768 -0.657586320
## [204,] 1.201683038 1.016703999 -1.617844139 1.145915109 -0.682858022
## [205,] -1.807181645 -0.673704761 -0.909165251 -0.542600144 -0.697323892
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## [208,] -0.721328123 0.145142743 1.245670834 -1.005611527 0.493983182
## [209,] -0.483839459 -0.454229646 0.058240719 -0.240884895 0.283251672
## [210,] 0.663630444 -2.030515942 1.095559877 -0.315653418 0.208334029
## [211,] 1.978468906 -1.541564858 0.344229726 0.254916972 0.343867249
## [212,] 2.937647970 0.023153745 -1.467099553 2.004769891 -0.185012738
## [213,] -0.086636710 1.891839624 1.573096232 0.223299508 -2.221106615
## [214,] -1.481813930 0.006331169 -1.173928063 -0.250137785 -0.112924714
## [215,] 0.623006822 -0.037759847 -0.710766534 0.184537311 -0.887891261
## [216,] 1.991882118 -1.666919941 -2.805934883 -0.871488718 0.175942738
## [217,] 0.744165906 -0.860059687 -1.328696095 1.365529752 0.751591017
## [218,] 0.641119818 -0.445632455 0.162013092 -2.055341520 0.923419949
## [219,] -1.586401627 -0.388025617 -1.097489991 -0.453696582 -0.661613141
## [220,] 4.773395918 2.278577670 -1.336404778 0.510730406 -1.718160684
## [221,] 2.921320323 -0.012042086 -1.874368061 -0.045263697 -0.566144677
## [222,] 0.503935335 1.035837075 -1.154051231 -0.866417161 0.131161351
## [223,] -1.241990069 0.411074638 1.790709487 0.707551103 0.092693855
## [224,] -0.133856941 -0.846749537 0.481837944 1.031203316 -0.200664046
## [225,] -1.486223026 -1.226757723 0.663500601 1.212738370 -0.747306389
## [226,] -0.762041381 1.164340422 1.896521625 1.074683686 0.812249845
## [227,] 2.005021660 0.341436716 -0.409217808 -0.832010193 0.147847697
## [228,] 1.814305601 1.684900471 0.545885187 -0.444700098 2.887385706
## [229,] -1.411373860 -0.029800132 -1.219717248 -0.012627251 -0.086502351
## [230,] -0.324175998 0.181346052 0.453617491 -1.500433205 -0.063295422
## [231,] -0.456860329 0.176546846 0.852740264 -0.298237857 0.679884046
## [232,] -1.210396528 0.443593233 -1.157566359 -0.418875718 -1.229168913
## [233,] 0.367888943 1.034558583 -0.899804344 -1.320083756 0.545063435
## [234,] -1.737267642 -0.768492804 -0.717586622 -0.042347936 -0.690091939
## [235,] -1.509987525 0.519084836 0.532663661 -0.793096619 -0.075050898
## [236,] -1.290446225 1.701929130 -0.262965485 -0.898972118 0.974935670
## [237,] 3.655612544 1.679581237 -0.078271387 0.366568656 -1.144046957
## [238,] 0.611276361 -1.193837776 1.025840807 -1.693775105 0.496074659
## [239,] 6.711875034 1.215508748 -1.279625142 0.587766000 -0.938041730
## [240,] -1.281390399 -0.456797389 0.383696463 1.327109609 -0.434647734
## [241,] 0.776720455 0.873249312 -0.255587193 0.950034593 1.789939090
## [242,] 0.008347450 1.173046306 1.625650682 -0.126758712 1.284764016
## [243,] -0.958826089 -0.492058288 0.745646701 -1.985299776 -0.313503201
## [244,] 1.609087788 0.768291741 1.106856868 1.288165361 -1.317902920
## [245,] 0.543831815 -0.344117364 1.084227436 0.743018250 -0.049164466
## [246,] -1.795501728 0.797766300 0.941073658 -0.948765046 0.188093947
## [247,] -2.078996209 0.034041364 0.343126833 -1.053156920 -0.428421322
## [248,] 0.486998129 0.122844418 -0.822868404 1.350720580 0.697385548
## [249,] -0.821657492 -0.011924402 0.873543779 1.971662603 0.110811955
## [250,] -1.398504155 -0.243599402 0.837410828 0.477686433 -0.150887846
## [251,] 0.526594325 -1.361027292 1.730491888 0.644317870 -0.904698848
## [252,] 0.120809384 -1.392425032 -0.882175385 0.251835439 0.060510736
## [253,] -0.289560811 -1.753881720 0.731478923 1.008115634 -0.564319747
## [254,] 2.350354264 -1.374432502 0.783487702 1.516771930 0.201694966
## [255,] 2.529945185 -0.796264796 -1.084229732 -1.768591624 1.468016449
## [256,] -0.594294620 0.606268901 0.546284310 -1.512570945 0.547901821
## [257,] -1.406577585 0.312852106 -0.020482861 0.091002001 -0.110026066
## [258,] -1.651971076 -0.143369845 -1.143133022 -0.250064542 -0.291778062
## [259,] 0.415871178 -0.214174686 0.915948123 0.956618386 0.974131542
## [260,] -0.286827613 -0.440600376 -0.511227621 -0.188717119 0.390008978
## [261,] -0.645411407 0.058506107 -2.305257330 2.581332331 0.223956712
## [262,] -0.628353063 -1.040695063 1.499765220 0.328717274 -0.091370940
## [263,] -0.136446586 -0.912547265 0.240795333 0.609862680 -0.011841605
## [264,] -1.777655604 -0.274014123 -1.028075306 -0.764011769 -0.961634321
## [265,] -1.357302997 2.288698502 1.019344070 -1.133889152 1.295074700
## [266,] -1.150407815 -1.178196185 0.453312973 -1.488628969 -0.550910191
## [267,] -0.854919366 2.319121839 -0.534036982 -0.401249649 1.590398378
## [268,] 1.748954057 -2.489466264 0.147763981 1.527744484 -0.031497689
## [269,] -0.738423976 -0.871268532 -1.716222096 -0.549433967 -0.141152979
## [270,] -0.346935263 1.923554748 -1.292856361 -0.360145431 -0.649527552
## [271,] 2.611945346 -0.868543943 -0.456914061 1.833405222 -0.121158473
## [272,] -0.054669716 0.467014101 -0.459580646 0.187565076 0.815668207
## [273,] 0.590763284 0.081986670 -0.821826225 1.066920091 0.715892272
## [274,] -0.771766282 0.497567733 -0.144543170 -0.043136586 -1.433593942
## [275,] 0.287407340 -0.999343796 -0.141647094 1.726767706 0.460339894
## [276,] -1.904210848 -0.711924915 -0.636156799 0.229311959 -0.732363166
## [277,] 1.980934953 -2.144737237 -1.558960290 -1.734660915 0.372677052
## [278,] 4.349982486 0.818990696 -1.850629065 0.156456507 -0.310120302
## [279,] -1.601460087 0.466219801 0.555412046 -1.282120597 -0.177034377
## [280,] 1.110817200 -0.894199685 0.626718163 -1.090577512 0.457144316
## [281,] -1.635586546 0.585764692 0.351472824 -0.436299965 0.162468184
## [282,] -0.910449829 -0.063109780 -0.243265787 1.440217859 -0.008738371
## [283,] 0.979721615 0.904442368 -1.232199254 1.008144535 -0.363957491
## [284,] -0.472435837 -0.521473629 0.942802823 0.140237047 0.029009438
## [285,] 0.298128461 -0.439838094 -0.230211394 0.045875504 0.466431500
## [286,] 0.876478490 -0.632485240 -2.150246922 0.523252544 -0.354676442
## [287,] 0.030556752 -0.246001099 -1.050954176 -0.130320899 0.416685941
## [288,] 0.489276289 0.149716001 1.343990756 -0.776952747 -1.363924275
## [289,] 1.167193218 4.324487587 0.744165112 -1.104452819 -2.960549114
## [290,] 5.639123713 1.493129585 0.436631086 0.391589194 1.328124017
## [291,] 0.076038156 2.149080398 1.231684279 -0.889701456 2.108001645
## [292,] -1.306362503 0.777428880 -0.836033189 -0.505010722 0.429704777
## [293,] -1.492629535 0.346667458 -1.594060891 -0.744201427 0.053005921
## [294,] 0.548191410 0.159332266 1.521957843 0.691090269 0.002822644
## [295,] 3.173294742 -0.713640891 1.483201289 -0.597042450 -0.955008287
## [296,] -1.711510331 0.207909220 -0.931632873 -0.732023246 -0.134887380
## [297,] -1.420928885 -1.297938310 0.314667960 1.070874265 -0.766364136
## [298,] -0.397038374 -0.140558009 -0.100049951 -1.210608408 -0.287822450
## [299,] -1.338159554 0.850035604 0.991498508 0.275292019 0.519975147
## [300,] 1.238726422 -0.682019739 -1.206227105 -1.584533216 0.599257188
## [301,] 0.476798036 -0.538294379 1.306977504 0.589987890 0.804993508
## [302,] 0.451358041 0.509847268 -0.404959275 1.025191596 1.150524367
## [303,] -0.410664267 1.809811675 0.163254213 1.203959868 1.107465182
## [304,] 0.631511135 4.553878477 0.617849698 -0.258625983 0.452803511
## [305,] 0.606275351 1.307303704 -1.190130416 -1.085147986 0.839582865
## [306,] 3.760469200 -1.318016453 -1.571659239 -0.958198521 -0.168654341
## [307,] 0.283257978 0.334225557 0.900109850 1.387190281 0.742119351
## [308,] 1.205872572 -1.025116718 -0.694241491 -0.489820821 0.185091372
## [309,] -0.547890175 -1.378267017 0.199506501 0.006777245 -0.282776412
## [310,] 0.675442079 -0.040092847 0.040280714 1.538300103 0.724233244
## [311,] -0.347420655 -1.297275709 -0.084885546 0.216594996 -0.374740492
## [312,] -1.082694803 1.058501944 -1.274637266 -0.535652316 -0.301170989
## [313,] -0.809911038 0.678119879 -0.193503870 0.489931605 -0.567989774
## [314,] 2.814192996 1.465015414 1.296910650 -1.024401483 -0.754090861
## [315,] -1.219216145 -0.216402526 0.775638956 0.706433637 -0.029531003
## [316,] -0.839858529 -1.160921154 -0.067522123 -0.376613864 -0.332337533
## [317,] 1.906604890 -1.476681383 -0.028831221 0.037013607 1.083914038
## [318,] -1.128786006 0.395890021 0.040446729 0.390323605 -0.149885563
## [319,] 4.980287452 1.400993226 0.386980437 0.646687478 -1.083846603
## [320,] -0.396555408 -0.215395452 -1.222389233 -0.813225124 0.424557329
## [321,] -1.686147468 0.664222126 1.210799613 -0.375476795 0.198108774
## [322,] -0.771587552 0.001912498 -0.021523533 2.182231316 0.393142757
## [323,] 2.121003409 -2.080663494 0.161998088 0.897550000 0.380306029
## [324,] 0.183525269 0.711131176 0.676974276 -0.837925098 -0.201495035
## [325,] -0.388480855 -0.019183155 -0.034180507 -0.379134234 0.583222451
## [326,] -0.270374270 0.372642009 0.619830911 -1.148519958 -0.407017698
## [327,] -0.016309255 -0.272150173 1.123754077 -0.347941297 -0.103237180
## [328,] -1.509365115 -1.227221931 0.110956778 1.437386493 -0.758506439
## [329,] 1.128006246 -1.746278013 0.499382396 -1.619420542 0.555724903
## [330,] -0.013678857 0.097843119 0.408072714 -0.795855347 -1.175223096
## [331,] 0.134239505 0.261168839 1.687827776 0.217195174 1.082628063
## [332,] 0.543266130 0.289044087 -1.889627887 1.415180585 1.063577278
## [333,] -1.694510184 -0.384164773 0.978956440 -0.619188118 -0.943767153
## [334,] -1.177192240 0.755347480 -0.072837954 0.262273753 0.532730202
## [335,] -0.154704801 -0.482019591 -0.130393501 0.108703255 0.455787032
## [336,] -1.222393212 -0.140605864 0.470903440 0.854635087 -0.236602493
## [337,] 0.985284375 -2.085350193 -0.309169317 -0.356636930 0.209646403
## [338,] 1.845084419 -1.284127961 -0.428328294 -1.460289251 0.838247554
## [339,] -1.537001279 1.111570387 0.652894920 -1.060718845 -0.002140100
## [340,] 0.486580696 -0.438599188 -0.143918334 0.966749788 0.107166844
## [341,] -0.381846642 -0.365594889 0.626052636 0.039508221 -0.092159877
## [342,] -1.058469609 1.839970213 -0.254329772 -0.731552164 -0.827823834
## [343,] 1.953784231 -1.229071105 0.160259672 0.867246394 1.295990204
## [344,] -1.632770525 -0.310017947 0.586575867 0.624972262 -0.312659105
## [345,] -0.069211481 1.179578849 -0.019456868 -1.025693279 0.424192027
## [346,] 0.924645953 0.318200997 -0.038558980 -0.176342543 -1.278270521
## [347,] -1.679627649 -0.870249748 1.201962925 0.638583744 -0.657934688
## [348,] -0.138978457 -0.327879510 1.445999742 0.018109114 0.324021275
## [349,] -0.306354427 2.443421548 0.256738595 0.723881262 0.004780055
## [350,] -1.082397105 0.511694553 0.396630701 0.376171916 0.200267508
## [351,] 1.560087096 -0.172608049 2.042673531 0.001387343 0.943307040
## [352,] 0.213890453 0.121650120 -0.363220480 0.143134581 0.251009799
## [353,] -1.243101129 -0.469575151 -1.404226113 1.148855158 -0.206147146
## [354,] -1.723673624 -0.628891973 1.215101216 0.822337346 -0.530509884
## [355,] -1.845736715 -1.246640827 1.218806001 0.592440275 -0.970712299
## [356,] -0.533908899 0.509703545 -1.010222476 -1.067833304 0.770760459
## [357,] -0.621852817 1.060330174 -0.185420284 0.974853637 0.788314716
## [358,] -0.663822556 -0.698693563 -1.437208451 -1.000964685 -0.267520648
## [359,] -1.464448793 -0.997923794 0.090438438 0.991886193 -0.619748924
## [360,] -1.523194528 1.088366756 -0.015584201 -1.071387626 0.484479318
## [361,] -0.249284791 -0.495162923 -0.888175969 0.194375075 0.137323234
## [362,] -0.978278825 0.745196276 1.673492426 0.624652999 0.677279063
## [363,] 2.298810986 -0.090143085 -0.751106742 -0.561856912 1.569191798
## [364,] -0.641761160 -1.573225212 0.960424847 -0.179437036 -0.696431558
## [365,] -1.237501132 -0.412442737 1.793811573 1.137104529 -0.371283677
## [366,] -1.157403928 0.923508573 -0.442026074 -0.884941552 -0.171459484
## [367,] -0.796933393 1.222876039 0.723404723 -0.237384378 -0.510118334
## [368,] 2.646899548 0.301553970 0.690593527 -2.443750630 0.663805037
## [369,] -0.178975454 -0.138624086 1.105283992 -1.499072183 -0.164055484
## [370,] -1.330874437 0.769296425 -0.127097036 -1.223980155 -0.869663470
## [371,] 0.785519987 2.132318925 0.981263612 -0.639682484 -0.035075161
## [372,] 4.528600634 -0.995996130 0.568209680 -0.292649916 -0.397415282
## [373,] -2.215387412 -0.717213408 0.437807288 -1.098624561 -0.945243579
## [374,] 0.852816653 0.697424945 -0.415247520 0.859928559 0.964247801
## [375,] 1.528575274 1.579100810 0.424898608 1.740887715 -0.368739736
## [376,] 1.052831636 0.469776583 0.746395631 -0.477473960 -1.373515237
## [377,] 3.308075529 -0.637217047 -0.361014725 -0.281269186 -0.462933899
## [378,] 0.145308323 -0.337470348 1.183817291 1.285154406 0.271835930
## [379,] -0.100434292 -0.148112235 0.886936726 0.259148546 0.704812541
## PC6
## [1,] 0.116709537
## [2,] 0.110173000
## [3,] 0.151011377
## [4,] -0.343807479
## [5,] -0.068417317
## [6,] -0.420280958
## [7,] 0.014839886
## [8,] 0.336718257
## [9,] -0.045952454
## [10,] 1.939826284
## [11,] -0.146897222
## [12,] 0.183314250
## [13,] 0.114162471
## [14,] -0.102727402
## [15,] 0.196911289
## [16,] -0.296960713
## [17,] -0.346683316
## [18,] 0.385229903
## [19,] 0.250212417
## [20,] 0.210997273
## [21,] 0.178758339
## [22,] -0.003801151
## [23,] 0.217319459
## [24,] -0.187966712
## [25,] -0.249408299
## [26,] 0.582504343
## [27,] -0.264956027
## [28,] -0.324073726
## [29,] 0.392690074
## [30,] 0.433561922
## [31,] -0.044052794
## [32,] -0.172924722
## [33,] -0.273046392
## [34,] -0.339264995
## [35,] 0.377235819
## [36,] -0.090271827
## [37,] 0.414287669
## [38,] -0.393701821
## [39,] 0.033505637
## [40,] 0.354862667
## [41,] 0.077217544
## [42,] -0.251343699
## [43,] 0.437209594
## [44,] 0.418033744
## [45,] 0.092143326
## [46,] 0.453442755
## [47,] 0.025217332
## [48,] -0.198309910
## [49,] 0.187074835
## [50,] 0.063584865
## [51,] 0.411945392
## [52,] 0.347020693
## [53,] -1.602200768
## [54,] -0.297652746
## [55,] 0.140534670
## [56,] -0.120117267
## [57,] 0.295188323
## [58,] -0.436240290
## [59,] -0.241532009
## [60,] -0.152644965
## [61,] -0.340782009
## [62,] -0.237639469
## [63,] 0.300926071
## [64,] -0.253457399
## [65,] -0.123036265
## [66,] -0.318934216
## [67,] 0.157579795
## [68,] -0.260813996
## [69,] -0.245354609
## [70,] -0.305254302
## [71,] -1.882250425
## [72,] 0.409598000
## [73,] 0.232202465
## [74,] -0.149057573
## [75,] 0.545903188
## [76,] 0.277588617
## [77,] 0.361912198
## [78,] -0.478016137
## [79,] -0.412381253
## [80,] -0.183130748
## [81,] 0.233456245
## [82,] -0.356154388
## [83,] 0.449569521
## [84,] -0.185788498
## [85,] -0.219609958
## [86,] -0.001711114
## [87,] -1.559617792
## [88,] -0.428893296
## [89,] -0.349853393
## [90,] 0.067731920
## [91,] 0.142796842
## [92,] -0.180830638
## [93,] 0.315292384
## [94,] 0.557663845
## [95,] -0.172373827
## [96,] 0.407727459
## [97,] 0.327538602
## [98,] 0.346056104
## [99,] 2.163269668
## [100,] 0.345529449
## [101,] 0.138719045
## [102,] -0.279523523
## [103,] -0.084975054
## [104,] 0.337408982
## [105,] 0.436700603
## [106,] 0.388716289
## [107,] 0.023800405
## [108,] -0.344894615
## [109,] 0.380430817
## [110,] 0.059212100
## [111,] -0.160062648
## [112,] 0.451808896
## [113,] -0.328134576
## [114,] -0.232509061
## [115,] 0.417691744
## [116,] -0.283499777
## [117,] -0.334241319
## [118,] -0.354492127
## [119,] 0.016626218
## [120,] 0.329368287
## [121,] 0.014802916
## [122,] 1.788209994
## [123,] -0.225290106
## [124,] -0.049381001
## [125,] -0.176037238
## [126,] -0.147416810
## [127,] 0.274931744
## [128,] -0.288402296
## [129,] -0.238830171
## [130,] -0.321394130
## [131,] -0.060804904
## [132,] -0.198430755
## [133,] -0.201882037
## [134,] -0.416230299
## [135,] -0.104823016
## [136,] -0.259292999
## [137,] 0.309515655
## [138,] 0.473433423
## [139,] -0.224455247
## [140,] -0.113549634
## [141,] -0.029270791
## [142,] -0.408139727
## [143,] -0.249679273
## [144,] 0.052432954
## [145,] 0.123609326
## [146,] 0.110721474
## [147,] 0.039482206
## [148,] -0.055563924
## [149,] -0.301541438
## [150,] 0.339761189
## [151,] -0.143565175
## [152,] 0.495882321
## [153,] -0.338275303
## [154,] -0.259013852
## [155,] -0.268105530
## [156,] -0.980893416
## [157,] -0.246803124
## [158,] -0.078306763
## [159,] 0.382030122
## [160,] 0.087323777
## [161,] 0.376505108
## [162,] 0.053401289
## [163,] -0.338300621
## [164,] -0.183747770
## [165,] 0.432642111
## [166,] 0.187719391
## [167,] -0.323645603
## [168,] 0.829006715
## [169,] 0.043491740
## [170,] -0.248046133
## [171,] -0.060255793
## [172,] -0.083545793
## [173,] -0.167508321
## [174,] -0.089468938
## [175,] -0.143831223
## [176,] 0.323860642
## [177,] -0.174432941
## [178,] -0.239734115
## [179,] 0.497289814
## [180,] -0.327540210
## [181,] -0.151688764
## [182,] 0.197182238
## [183,] -0.042715485
## [184,] 0.044010655
## [185,] -0.925270972
## [186,] 0.322942444
## [187,] -0.036587651
## [188,] 0.356359819
## [189,] 0.423139332
## [190,] -0.257850948
## [191,] 0.463686146
## [192,] -0.032295644
## [193,] -0.221120598
## [194,] 0.347410914
## [195,] -0.102882758
## [196,] -0.052886406
## [197,] 0.099771649
## [198,] 0.161046943
## [199,] 0.245795874
## [200,] 0.272924190
## [201,] 0.339839246
## [202,] 0.395294558
## [203,] -0.065386536
## [204,] 0.561844444
## [205,] -0.271407182
## [206,] -0.059059407
## [207,] 0.083045883
## [208,] 0.377344777
## [209,] 0.334594979
## [210,] 2.210117773
## [211,] -0.225352991
## [212,] 0.659498155
## [213,] 0.005821771
## [214,] -0.246898562
## [215,] 0.168733702
## [216,] -0.366893261
## [217,] -0.293117425
## [218,] 0.423293245
## [219,] -0.277523269
## [220,] 0.108760866
## [221,] 0.070710680
## [222,] 0.163384108
## [223,] -0.232906221
## [224,] 0.408184032
## [225,] -0.300209061
## [226,] -0.343281023
## [227,] 0.380266460
## [228,] 0.475769439
## [229,] -0.240418547
## [230,] 0.118544474
## [231,] 0.411577815
## [232,] -0.017746096
## [233,] -0.022662183
## [234,] -0.215224961
## [235,] -0.336453644
## [236,] -0.208327609
## [237,] 0.415886191
## [238,] 0.260849310
## [239,] -0.336942900
## [240,] -0.122484819
## [241,] -0.025660118
## [242,] 0.330693931
## [243,] 0.187450418
## [244,] 0.092254142
## [245,] -0.103389100
## [246,] -0.135338511
## [247,] -0.081072198
## [248,] 0.345962874
## [249,] -0.250967381
## [250,] -0.344899324
## [251,] -0.429960219
## [252,] -0.282830186
## [253,] 0.174435063
## [254,] -0.002994835
## [255,] -1.217412358
## [256,] 0.360421127
## [257,] -0.146287428
## [258,] -0.133025274
## [259,] -0.126146676
## [260,] 0.220778323
## [261,] 0.108029807
## [262,] 0.349752615
## [263,] 0.200005121
## [264,] -0.101933578
## [265,] -0.161334026
## [266,] 0.285586865
## [267,] -0.238563544
## [268,] 0.083679922
## [269,] 0.509906873
## [270,] -0.146139621
## [271,] 0.334416111
## [272,] 0.473647831
## [273,] 0.136442835
## [274,] -0.251405937
## [275,] 0.114366181
## [276,] 0.048022334
## [277,] -1.054946234
## [278,] -0.700681151
## [279,] -0.434292485
## [280,] 0.255500421
## [281,] -0.124820953
## [282,] -0.258508925
## [283,] 0.519297048
## [284,] 0.418680932
## [285,] -0.218443452
## [286,] -0.216123751
## [287,] 0.115923969
## [288,] -0.027866918
## [289,] -0.058716464
## [290,] -2.000384525
## [291,] 0.277974900
## [292,] -0.293421787
## [293,] -0.259635342
## [294,] 0.059625913
## [295,] 0.971487465
## [296,] -0.150615259
## [297,] -0.400937784
## [298,] 0.238954410
## [299,] -0.144937084
## [300,] 0.201952185
## [301,] -0.447834040
## [302,] 0.281901496
## [303,] -0.203869133
## [304,] -0.134202490
## [305,] -0.059036104
## [306,] -1.689975498
## [307,] 0.458648969
## [308,] 0.521154125
## [309,] 0.178933466
## [310,] 0.097184547
## [311,] 0.178727506
## [312,] -0.114849810
## [313,] -0.177928676
## [314,] 0.278091472
## [315,] -0.424718686
## [316,] 0.421376781
## [317,] -0.381796482
## [318,] -0.221941061
## [319,] -0.754255469
## [320,] 0.249838558
## [321,] -0.111526776
## [322,] -0.207650126
## [323,] -0.362767449
## [324,] 0.207891984
## [325,] 0.340268457
## [326,] 0.368766457
## [327,] 0.012058601
## [328,] -0.149559490
## [329,] 1.463155184
## [330,] 0.382942476
## [331,] -0.032112095
## [332,] 0.397084457
## [333,] -0.354911460
## [334,] -0.233823936
## [335,] 0.146812456
## [336,] -0.250028422
## [337,] 0.205107833
## [338,] -0.667916271
## [339,] -0.159417162
## [340,] 0.044940196
## [341,] 0.444365443
## [342,] 0.218371896
## [343,] -0.083864131
## [344,] -0.066718642
## [345,] 0.460637350
## [346,] 0.010040209
## [347,] -0.249703684
## [348,] 0.069849151
## [349,] 0.133553509
## [350,] -0.337335972
## [351,] 0.358285729
## [352,] 0.221064477
## [353,] -0.125296735
## [354,] -0.070458295
## [355,] -0.224997131
## [356,] 0.501370980
## [357,] -0.349367892
## [358,] 0.380452253
## [359,] -0.271394600
## [360,] -0.258419685
## [361,] 0.402658885
## [362,] -0.468027915
## [363,] -0.324990632
## [364,] 0.142034987
## [365,] -0.347928412
## [366,] -0.351391164
## [367,] -0.285977778
## [368,] -0.971457197
## [369,] -0.181523245
## [370,] -0.240725882
## [371,] 0.387573331
## [372,] -0.229079837
## [373,] -0.209054420
## [374,] 0.036780440
## [375,] 0.503922523
## [376,] -0.173505314
## [377,] -0.787406645
## [378,] 0.319960047
## [379,] 0.154968029
plot(Cancer_pca$x,xlim=xlim,ylim=xlim)
Cancer_pca$rotation[,1]
## Age Stage Tumor Size
## -0.2153849 0.5628689 0.5822135
## Regional Node Examined Reginol Node Positive Survival Months
## 0.2375181 0.4590407 -0.1751633
Cancer_pca$rotation
## PC1 PC2 PC3 PC4
## Age -0.2153849 0.21608166 -0.34917081 -0.88535662
## Stage 0.5628689 -0.32693628 0.06177527 -0.24457235
## Tumor Size 0.5822135 -0.28223117 -0.01433325 -0.21375444
## Regional Node Examined 0.2375181 0.75305159 0.21117279 0.02093686
## Reginol Node Positive 0.4590407 0.43924020 0.01680220 0.01827332
## Survival Months -0.1751633 -0.08214803 0.91059423 -0.33145859
## PC5 PC6
## Age -0.03346239 0.004663803
## Stage 0.18847337 0.690751203
## Tumor Size 0.13490974 -0.719218983
## Regional Node Examined 0.57570300 -0.005676451
## Reginol Node Positive -0.77028208 0.048979548
## Survival Months -0.14279002 -0.055980895
plot(Cancer[,-1])
Cancer_pca$x
## PC1 PC2 PC3 PC4 PC5
## [1,] -1.493744354 1.672703734 -0.797771118 -0.639380539 0.852277723
## [2,] 0.426322428 -0.124086338 -0.222112841 0.478038848 -0.014925567
## [3,] 1.694207768 -0.545124348 0.069937198 -1.032701826 -0.039058417
## [4,] -1.767583528 -0.885302494 -0.030847119 -0.208720400 -0.771910136
## [5,] 0.043714825 -1.603388200 -0.903121553 0.849669634 -0.078371793
## [6,] -1.028534021 0.502739380 0.863904840 0.421284750 0.233248754
## [7,] -1.338771984 0.023023987 -0.740136022 1.021953281 0.038121315
## [8,] 0.406514411 -0.944219552 -1.935001240 2.169992691 0.548288673
## [9,] 4.993025728 -0.305103355 0.801778453 0.176933443 -0.724303190
## [10,] 1.937948477 0.689507346 0.639790414 -2.348269489 -0.376692694
## [11,] -1.756901401 0.140915113 -1.036789014 -0.816405788 -0.204199065
## [12,] 1.296312778 -1.473829054 1.127778467 -0.112920985 0.266696937
## [13,] -0.090142691 -0.016296775 -1.070302648 -0.891412586 0.200775716
## [14,] -0.076244034 1.581531699 -0.943407970 1.540387096 0.141353261
## [15,] 1.004107956 1.120512340 -0.515080564 -0.672554789 -1.296448032
## [16,] -1.005634503 0.998331229 -1.092830786 0.057925043 0.742413832
## [17,] -0.538374841 -1.839056096 0.934166263 -0.882076640 -0.578346113
## [18,] 0.204445317 0.244548369 0.249012257 1.256474649 1.134795943
## [19,] -0.419443766 -0.379535399 1.728764442 0.083365143 0.402986436
## [20,] -0.252782392 0.344103196 0.155613436 -0.655869450 0.860603335
## [21,] -0.036353656 -0.349284099 0.645811404 0.425442619 0.372107468
## [22,] 0.504291512 0.121502823 -0.952996651 -0.061329141 0.135596833
## [23,] -0.618672209 -1.285043286 -0.036105811 -0.229784303 -0.280109421
## [24,] 1.459334722 -1.104003050 1.630015919 -0.538883137 1.064729564
## [25,] 0.693501261 3.217631237 1.088615995 -0.680914229 -2.330312186
## [26,] 1.342457422 2.945510521 0.104659090 -0.694326558 -0.785747318
## [27,] 2.475721782 2.107120006 1.821692902 0.042150966 -2.125689786
## [28,] -1.137184838 -0.018509243 0.662500068 1.019754895 0.143564512
## [29,] -0.082096727 0.062026127 -0.404849247 -0.143815038 0.043817854
## [30,] -0.951459346 -0.397603334 0.033425845 -1.324785280 0.016907630
## [31,] 0.004306142 -1.599200390 -0.821234717 0.828802331 -0.096628489
## [32,] -1.358590305 -0.557530387 -1.182191573 0.826013095 -0.330970546
## [33,] -1.790419403 -0.472260893 0.282426323 -0.357402908 -0.542183270
## [34,] -0.908445651 0.994824271 -0.546660828 -0.042005466 0.292432820
## [35,] 1.245709794 0.857794242 -1.178327309 1.397760831 -0.230660457
## [36,] -1.439873416 -0.186081367 0.144133667 0.662537801 -0.393665514
## [37,] 0.636390371 0.900377415 -1.197745317 0.553485818 0.437914429
## [38,] -1.304428696 0.097530771 1.328492259 0.221100925 -0.155155562
## [39,] -0.097417933 -0.858136005 0.513336501 0.257353363 0.029439452
## [40,] -0.188925650 -0.025716107 1.521237025 -0.147451873 -0.286733286
## [41,] 2.535953943 -0.283072938 -1.273811462 -0.496124138 -0.691155605
## [42,] -1.364589888 0.380987232 -0.926166470 -0.409214549 -0.084453563
## [43,] -1.095258604 -1.245692755 -0.025636708 -0.959504567 -0.544787256
## [44,] 0.018958421 0.185171532 0.594724325 -0.026225609 -0.312285920
## [45,] -1.483766860 0.205593899 -0.521531513 0.532329976 -0.202487124
## [46,] 0.803570710 -0.823728790 0.269737583 -1.940110944 -0.213877418
## [47,] -0.776759752 0.318065419 -0.898736044 2.118307298 0.308120927
## [48,] -1.440160549 0.277491231 -0.933452622 -0.172656258 0.076695703
## [49,] 0.550199236 0.443259288 0.544534206 -0.061726221 -0.634281043
## [50,] -1.959716237 0.269905907 -0.358261698 -1.104900464 -0.742921582
## [51,] 0.283946083 -0.215989222 0.718462913 1.705505213 0.429398197
## [52,] 0.584420507 -1.170636855 -0.658910102 -2.000608348 0.454750957
## [53,] 2.164109035 -2.375151885 0.202704168 -1.926001263 0.605914036
## [54,] 1.673683848 -0.438611018 -0.189966395 -1.566014043 1.244480037
## [55,] -1.630123732 0.631351549 -0.019980046 0.212113815 0.215871580
## [56,] -1.450559221 0.201501035 -0.069005014 0.333630589 0.063005452
## [57,] -0.534036352 0.291756051 0.624478817 -1.023860005 0.669994233
## [58,] -0.354843129 3.274197111 2.410035980 0.361353654 2.502769179
## [59,] -1.178588655 0.226034827 0.171909908 0.786762124 0.247357475
## [60,] -1.248535425 0.638963394 0.202025885 0.279803670 0.179044984
## [61,] -0.944827480 1.241989527 0.467351263 0.104831170 0.693575290
## [62,] -1.056029210 0.031887224 -0.922233051 1.020017722 0.191600412
## [63,] -0.473763736 -1.839525046 0.381440310 1.043813308 -0.465299021
## [64,] 1.681009012 -0.528168820 0.166784745 -1.236306623 1.216190250
## [65,] -1.312786276 0.965097163 -0.969708882 -0.635102168 0.024970627
## [66,] -1.639877002 -0.931529988 1.401477586 0.658502060 -0.668767345
## [67,] 4.455166578 1.087532562 0.124772958 2.053348449 -1.489900944
## [68,] -0.707613499 0.590986037 1.179291019 1.595111891 0.263308423
## [69,] -1.710632794 -0.549715482 -0.153074842 -0.100695874 -0.540451474
## [70,] -1.171903123 0.100583865 0.469100757 0.412780064 -0.339388614
## [71,] 3.302612150 -1.737283578 1.502810946 -1.179097587 -0.118238924
## [72,] 2.121655213 2.644141124 -2.473204090 -0.044893038 -1.314192531
## [73,] 0.528823585 -0.636078944 0.137430927 2.495082814 0.843161685
## [74,] -1.868775707 0.569029628 0.581800057 -1.084485611 0.002065102
## [75,] 0.683905846 1.767290796 0.241693051 -1.337566812 -1.608284497
## [76,] 0.821006546 -1.188104492 0.917466077 -1.089980478 0.637354405
## [77,] -0.499967072 -0.063567628 -0.217092609 -1.242667319 -0.300754296
## [78,] 0.056071716 -1.653376800 1.664161542 0.435774870 -0.079376450
## [79,] 0.099588612 -1.161140621 0.358003056 -0.058098223 0.191212303
## [80,] -1.638985742 0.150875793 -1.403816856 -0.700686152 -0.135813445
## [81,] 0.865297254 1.214733944 1.463461173 -0.297882350 -1.014695877
## [82,] -1.545124764 0.127252910 -0.935729044 -0.793110208 -0.096332740
## [83,] -0.757282603 -0.365269832 -0.559376514 -1.125365040 -0.112495907
## [84,] -1.494668798 -0.862217669 -1.017557513 0.729371690 -0.585327071
## [85,] -1.198962297 0.090483632 -0.244225721 0.803338834 0.150630291
## [86,] 1.053228198 0.023027292 0.260206980 0.703883631 -1.086933498
## [87,] 2.839883593 -2.296312935 0.510353279 -0.693661524 0.066738128
## [88,] 1.506058603 -1.812772768 0.528733408 -0.767001468 0.643656650
## [89,] -1.539415867 -0.136768478 0.768955037 -0.049503375 -0.188258747
## [90,] -2.166532837 0.071753733 0.343483494 -0.898166612 -0.445936393
## [91,] 0.893002750 -1.772886261 0.734063638 -0.797845672 0.341156668
## [92,] -0.677904182 -0.104397875 0.169469929 2.673756815 0.405882517
## [93,] -0.646604416 -0.740495104 0.063231982 -1.095809541 -0.767513218
## [94,] 1.683330979 1.567742424 -0.698706197 1.431672587 -1.080548515
## [95,] -1.509921397 0.297490480 0.490010821 -0.323083740 -0.437095352
## [96,] -0.135237286 0.293266912 -1.015571227 -0.225694168 0.642455326
## [97,] 0.027644129 -1.133291443 -1.997458759 1.032137750 -0.070625404
## [98,] -0.637273583 -0.513850978 -0.306967375 -0.684532247 0.140054208
## [99,] 1.070049729 -2.036508976 -0.316339810 -0.094341352 -0.094161935
## [100,] -0.455435814 0.089328755 -1.403983913 -1.027093674 0.560281943
## [101,] 4.600390311 2.244846920 0.532264308 1.259266636 -1.010942778
## [102,] -0.787145836 1.086091949 0.549806202 1.093912587 0.984179992
## [103,] 0.655142324 -1.683984928 -2.308143986 2.208715115 0.240582243
## [104,] -0.428540034 -0.840500324 -1.048098702 -0.027665882 0.077046929
## [105,] -0.110654721 -0.123171275 -0.175937919 0.338031509 0.196792323
## [106,] -0.734249607 -1.236231879 -1.090037416 -0.386975718 -0.336972535
## [107,] 0.296584193 -0.577728068 -2.014640498 0.588158511 0.632602330
## [108,] -1.410702952 0.429684625 -0.958296105 -0.866024725 -0.101651534
## [109,] -0.418905210 -1.232525386 1.863199813 1.081316900 -0.304585111
## [110,] 0.446752555 1.508585940 -0.342268303 -0.736468382 1.406332814
## [111,] -1.134059417 0.782686222 -0.521004605 -0.152263500 -0.210024740
## [112,] 1.181466882 -2.299898160 0.735344703 0.997333267 -0.237945040
## [113,] 1.830654533 1.883074076 0.954309940 0.626252247 0.685943765
## [114,] 0.454774207 -0.643039459 0.237045213 0.759165544 0.470129822
## [115,] 0.864920996 -1.531113286 1.149483739 -0.984234084 -0.541097522
## [116,] -0.897625868 0.218458064 -0.870977930 0.772271080 -0.128040261
## [117,] 1.357865125 -1.941049776 0.946671254 -0.674767960 0.499517827
## [118,] -0.915336154 1.327339693 0.352068802 -1.370754921 -1.073206670
## [119,] 0.094948933 -0.356826249 1.052712045 0.237447671 0.183785081
## [120,] -0.037442692 -0.108870167 -0.518461408 0.323952099 0.490323176
## [121,] -0.703244230 -0.760629115 0.236405707 -1.666145723 -0.328854978
## [122,] 1.727474232 -1.256161661 0.911292089 0.280268540 0.754418800
## [123,] 1.839479021 0.845697621 -0.141543565 0.392072998 -1.461521820
## [124,] 0.275373090 0.726740366 0.643511448 -0.752337791 0.616212060
## [125,] -0.732974709 1.225314046 -0.703247765 0.876777966 0.813571603
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## [168,] 4.057107584 0.177251126 2.338537102 0.287960419 -0.658831067
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## [186,] -0.646848816 0.019961075 0.140097904 -1.345604301 0.174968361
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## [188,] -0.341629561 -0.113562351 -0.165011337 -0.351171147 0.299781146
## [189,] 0.597265999 2.425823378 1.007898127 -0.923443496 0.528966635
## [190,] -1.161264597 0.015537197 0.541717900 1.081599330 0.151672237
## [191,] -0.477014120 -0.313853416 -0.666580443 -0.171072190 0.361420355
## [192,] -2.115125949 -0.729760082 0.102680575 -0.379831150 -0.871667253
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## [194,] -0.707735717 -1.202340369 0.313311997 -0.079193489 -0.266559479
## [195,] 3.115036491 -0.278203347 -0.068038843 0.730365425 -0.555712164
## [196,] -1.696392904 -0.279442921 -1.520016658 -0.119474656 -0.395871345
## [197,] 0.151090645 -0.052353299 -0.654184084 0.093232715 0.611872104
## [198,] 1.330786502 -1.333832490 1.198984292 -0.592071242 -0.156910522
## [199,] 0.296675856 0.507260694 -0.459773048 0.471858283 1.040250209
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## [202,] -0.085308348 0.324848824 -0.506897761 -0.413457726 0.183316995
## [203,] -1.822877611 -0.578840959 -1.943795566 -0.354374768 -0.657586320
## [204,] 1.201683038 1.016703999 -1.617844139 1.145915109 -0.682858022
## [205,] -1.807181645 -0.673704761 -0.909165251 -0.542600144 -0.697323892
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## [211,] 1.978468906 -1.541564858 0.344229726 0.254916972 0.343867249
## [212,] 2.937647970 0.023153745 -1.467099553 2.004769891 -0.185012738
## [213,] -0.086636710 1.891839624 1.573096232 0.223299508 -2.221106615
## [214,] -1.481813930 0.006331169 -1.173928063 -0.250137785 -0.112924714
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## [216,] 1.991882118 -1.666919941 -2.805934883 -0.871488718 0.175942738
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## [219,] -1.586401627 -0.388025617 -1.097489991 -0.453696582 -0.661613141
## [220,] 4.773395918 2.278577670 -1.336404778 0.510730406 -1.718160684
## [221,] 2.921320323 -0.012042086 -1.874368061 -0.045263697 -0.566144677
## [222,] 0.503935335 1.035837075 -1.154051231 -0.866417161 0.131161351
## [223,] -1.241990069 0.411074638 1.790709487 0.707551103 0.092693855
## [224,] -0.133856941 -0.846749537 0.481837944 1.031203316 -0.200664046
## [225,] -1.486223026 -1.226757723 0.663500601 1.212738370 -0.747306389
## [226,] -0.762041381 1.164340422 1.896521625 1.074683686 0.812249845
## [227,] 2.005021660 0.341436716 -0.409217808 -0.832010193 0.147847697
## [228,] 1.814305601 1.684900471 0.545885187 -0.444700098 2.887385706
## [229,] -1.411373860 -0.029800132 -1.219717248 -0.012627251 -0.086502351
## [230,] -0.324175998 0.181346052 0.453617491 -1.500433205 -0.063295422
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## [232,] -1.210396528 0.443593233 -1.157566359 -0.418875718 -1.229168913
## [233,] 0.367888943 1.034558583 -0.899804344 -1.320083756 0.545063435
## [234,] -1.737267642 -0.768492804 -0.717586622 -0.042347936 -0.690091939
## [235,] -1.509987525 0.519084836 0.532663661 -0.793096619 -0.075050898
## [236,] -1.290446225 1.701929130 -0.262965485 -0.898972118 0.974935670
## [237,] 3.655612544 1.679581237 -0.078271387 0.366568656 -1.144046957
## [238,] 0.611276361 -1.193837776 1.025840807 -1.693775105 0.496074659
## [239,] 6.711875034 1.215508748 -1.279625142 0.587766000 -0.938041730
## [240,] -1.281390399 -0.456797389 0.383696463 1.327109609 -0.434647734
## [241,] 0.776720455 0.873249312 -0.255587193 0.950034593 1.789939090
## [242,] 0.008347450 1.173046306 1.625650682 -0.126758712 1.284764016
## [243,] -0.958826089 -0.492058288 0.745646701 -1.985299776 -0.313503201
## [244,] 1.609087788 0.768291741 1.106856868 1.288165361 -1.317902920
## [245,] 0.543831815 -0.344117364 1.084227436 0.743018250 -0.049164466
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## [247,] -2.078996209 0.034041364 0.343126833 -1.053156920 -0.428421322
## [248,] 0.486998129 0.122844418 -0.822868404 1.350720580 0.697385548
## [249,] -0.821657492 -0.011924402 0.873543779 1.971662603 0.110811955
## [250,] -1.398504155 -0.243599402 0.837410828 0.477686433 -0.150887846
## [251,] 0.526594325 -1.361027292 1.730491888 0.644317870 -0.904698848
## [252,] 0.120809384 -1.392425032 -0.882175385 0.251835439 0.060510736
## [253,] -0.289560811 -1.753881720 0.731478923 1.008115634 -0.564319747
## [254,] 2.350354264 -1.374432502 0.783487702 1.516771930 0.201694966
## [255,] 2.529945185 -0.796264796 -1.084229732 -1.768591624 1.468016449
## [256,] -0.594294620 0.606268901 0.546284310 -1.512570945 0.547901821
## [257,] -1.406577585 0.312852106 -0.020482861 0.091002001 -0.110026066
## [258,] -1.651971076 -0.143369845 -1.143133022 -0.250064542 -0.291778062
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## [260,] -0.286827613 -0.440600376 -0.511227621 -0.188717119 0.390008978
## [261,] -0.645411407 0.058506107 -2.305257330 2.581332331 0.223956712
## [262,] -0.628353063 -1.040695063 1.499765220 0.328717274 -0.091370940
## [263,] -0.136446586 -0.912547265 0.240795333 0.609862680 -0.011841605
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## [266,] -1.150407815 -1.178196185 0.453312973 -1.488628969 -0.550910191
## [267,] -0.854919366 2.319121839 -0.534036982 -0.401249649 1.590398378
## [268,] 1.748954057 -2.489466264 0.147763981 1.527744484 -0.031497689
## [269,] -0.738423976 -0.871268532 -1.716222096 -0.549433967 -0.141152979
## [270,] -0.346935263 1.923554748 -1.292856361 -0.360145431 -0.649527552
## [271,] 2.611945346 -0.868543943 -0.456914061 1.833405222 -0.121158473
## [272,] -0.054669716 0.467014101 -0.459580646 0.187565076 0.815668207
## [273,] 0.590763284 0.081986670 -0.821826225 1.066920091 0.715892272
## [274,] -0.771766282 0.497567733 -0.144543170 -0.043136586 -1.433593942
## [275,] 0.287407340 -0.999343796 -0.141647094 1.726767706 0.460339894
## [276,] -1.904210848 -0.711924915 -0.636156799 0.229311959 -0.732363166
## [277,] 1.980934953 -2.144737237 -1.558960290 -1.734660915 0.372677052
## [278,] 4.349982486 0.818990696 -1.850629065 0.156456507 -0.310120302
## [279,] -1.601460087 0.466219801 0.555412046 -1.282120597 -0.177034377
## [280,] 1.110817200 -0.894199685 0.626718163 -1.090577512 0.457144316
## [281,] -1.635586546 0.585764692 0.351472824 -0.436299965 0.162468184
## [282,] -0.910449829 -0.063109780 -0.243265787 1.440217859 -0.008738371
## [283,] 0.979721615 0.904442368 -1.232199254 1.008144535 -0.363957491
## [284,] -0.472435837 -0.521473629 0.942802823 0.140237047 0.029009438
## [285,] 0.298128461 -0.439838094 -0.230211394 0.045875504 0.466431500
## [286,] 0.876478490 -0.632485240 -2.150246922 0.523252544 -0.354676442
## [287,] 0.030556752 -0.246001099 -1.050954176 -0.130320899 0.416685941
## [288,] 0.489276289 0.149716001 1.343990756 -0.776952747 -1.363924275
## [289,] 1.167193218 4.324487587 0.744165112 -1.104452819 -2.960549114
## [290,] 5.639123713 1.493129585 0.436631086 0.391589194 1.328124017
## [291,] 0.076038156 2.149080398 1.231684279 -0.889701456 2.108001645
## [292,] -1.306362503 0.777428880 -0.836033189 -0.505010722 0.429704777
## [293,] -1.492629535 0.346667458 -1.594060891 -0.744201427 0.053005921
## [294,] 0.548191410 0.159332266 1.521957843 0.691090269 0.002822644
## [295,] 3.173294742 -0.713640891 1.483201289 -0.597042450 -0.955008287
## [296,] -1.711510331 0.207909220 -0.931632873 -0.732023246 -0.134887380
## [297,] -1.420928885 -1.297938310 0.314667960 1.070874265 -0.766364136
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## [299,] -1.338159554 0.850035604 0.991498508 0.275292019 0.519975147
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## [302,] 0.451358041 0.509847268 -0.404959275 1.025191596 1.150524367
## [303,] -0.410664267 1.809811675 0.163254213 1.203959868 1.107465182
## [304,] 0.631511135 4.553878477 0.617849698 -0.258625983 0.452803511
## [305,] 0.606275351 1.307303704 -1.190130416 -1.085147986 0.839582865
## [306,] 3.760469200 -1.318016453 -1.571659239 -0.958198521 -0.168654341
## [307,] 0.283257978 0.334225557 0.900109850 1.387190281 0.742119351
## [308,] 1.205872572 -1.025116718 -0.694241491 -0.489820821 0.185091372
## [309,] -0.547890175 -1.378267017 0.199506501 0.006777245 -0.282776412
## [310,] 0.675442079 -0.040092847 0.040280714 1.538300103 0.724233244
## [311,] -0.347420655 -1.297275709 -0.084885546 0.216594996 -0.374740492
## [312,] -1.082694803 1.058501944 -1.274637266 -0.535652316 -0.301170989
## [313,] -0.809911038 0.678119879 -0.193503870 0.489931605 -0.567989774
## [314,] 2.814192996 1.465015414 1.296910650 -1.024401483 -0.754090861
## [315,] -1.219216145 -0.216402526 0.775638956 0.706433637 -0.029531003
## [316,] -0.839858529 -1.160921154 -0.067522123 -0.376613864 -0.332337533
## [317,] 1.906604890 -1.476681383 -0.028831221 0.037013607 1.083914038
## [318,] -1.128786006 0.395890021 0.040446729 0.390323605 -0.149885563
## [319,] 4.980287452 1.400993226 0.386980437 0.646687478 -1.083846603
## [320,] -0.396555408 -0.215395452 -1.222389233 -0.813225124 0.424557329
## [321,] -1.686147468 0.664222126 1.210799613 -0.375476795 0.198108774
## [322,] -0.771587552 0.001912498 -0.021523533 2.182231316 0.393142757
## [323,] 2.121003409 -2.080663494 0.161998088 0.897550000 0.380306029
## [324,] 0.183525269 0.711131176 0.676974276 -0.837925098 -0.201495035
## [325,] -0.388480855 -0.019183155 -0.034180507 -0.379134234 0.583222451
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## [327,] -0.016309255 -0.272150173 1.123754077 -0.347941297 -0.103237180
## [328,] -1.509365115 -1.227221931 0.110956778 1.437386493 -0.758506439
## [329,] 1.128006246 -1.746278013 0.499382396 -1.619420542 0.555724903
## [330,] -0.013678857 0.097843119 0.408072714 -0.795855347 -1.175223096
## [331,] 0.134239505 0.261168839 1.687827776 0.217195174 1.082628063
## [332,] 0.543266130 0.289044087 -1.889627887 1.415180585 1.063577278
## [333,] -1.694510184 -0.384164773 0.978956440 -0.619188118 -0.943767153
## [334,] -1.177192240 0.755347480 -0.072837954 0.262273753 0.532730202
## [335,] -0.154704801 -0.482019591 -0.130393501 0.108703255 0.455787032
## [336,] -1.222393212 -0.140605864 0.470903440 0.854635087 -0.236602493
## [337,] 0.985284375 -2.085350193 -0.309169317 -0.356636930 0.209646403
## [338,] 1.845084419 -1.284127961 -0.428328294 -1.460289251 0.838247554
## [339,] -1.537001279 1.111570387 0.652894920 -1.060718845 -0.002140100
## [340,] 0.486580696 -0.438599188 -0.143918334 0.966749788 0.107166844
## [341,] -0.381846642 -0.365594889 0.626052636 0.039508221 -0.092159877
## [342,] -1.058469609 1.839970213 -0.254329772 -0.731552164 -0.827823834
## [343,] 1.953784231 -1.229071105 0.160259672 0.867246394 1.295990204
## [344,] -1.632770525 -0.310017947 0.586575867 0.624972262 -0.312659105
## [345,] -0.069211481 1.179578849 -0.019456868 -1.025693279 0.424192027
## [346,] 0.924645953 0.318200997 -0.038558980 -0.176342543 -1.278270521
## [347,] -1.679627649 -0.870249748 1.201962925 0.638583744 -0.657934688
## [348,] -0.138978457 -0.327879510 1.445999742 0.018109114 0.324021275
## [349,] -0.306354427 2.443421548 0.256738595 0.723881262 0.004780055
## [350,] -1.082397105 0.511694553 0.396630701 0.376171916 0.200267508
## [351,] 1.560087096 -0.172608049 2.042673531 0.001387343 0.943307040
## [352,] 0.213890453 0.121650120 -0.363220480 0.143134581 0.251009799
## [353,] -1.243101129 -0.469575151 -1.404226113 1.148855158 -0.206147146
## [354,] -1.723673624 -0.628891973 1.215101216 0.822337346 -0.530509884
## [355,] -1.845736715 -1.246640827 1.218806001 0.592440275 -0.970712299
## [356,] -0.533908899 0.509703545 -1.010222476 -1.067833304 0.770760459
## [357,] -0.621852817 1.060330174 -0.185420284 0.974853637 0.788314716
## [358,] -0.663822556 -0.698693563 -1.437208451 -1.000964685 -0.267520648
## [359,] -1.464448793 -0.997923794 0.090438438 0.991886193 -0.619748924
## [360,] -1.523194528 1.088366756 -0.015584201 -1.071387626 0.484479318
## [361,] -0.249284791 -0.495162923 -0.888175969 0.194375075 0.137323234
## [362,] -0.978278825 0.745196276 1.673492426 0.624652999 0.677279063
## [363,] 2.298810986 -0.090143085 -0.751106742 -0.561856912 1.569191798
## [364,] -0.641761160 -1.573225212 0.960424847 -0.179437036 -0.696431558
## [365,] -1.237501132 -0.412442737 1.793811573 1.137104529 -0.371283677
## [366,] -1.157403928 0.923508573 -0.442026074 -0.884941552 -0.171459484
## [367,] -0.796933393 1.222876039 0.723404723 -0.237384378 -0.510118334
## [368,] 2.646899548 0.301553970 0.690593527 -2.443750630 0.663805037
## [369,] -0.178975454 -0.138624086 1.105283992 -1.499072183 -0.164055484
## [370,] -1.330874437 0.769296425 -0.127097036 -1.223980155 -0.869663470
## [371,] 0.785519987 2.132318925 0.981263612 -0.639682484 -0.035075161
## [372,] 4.528600634 -0.995996130 0.568209680 -0.292649916 -0.397415282
## [373,] -2.215387412 -0.717213408 0.437807288 -1.098624561 -0.945243579
## [374,] 0.852816653 0.697424945 -0.415247520 0.859928559 0.964247801
## [375,] 1.528575274 1.579100810 0.424898608 1.740887715 -0.368739736
## [376,] 1.052831636 0.469776583 0.746395631 -0.477473960 -1.373515237
## [377,] 3.308075529 -0.637217047 -0.361014725 -0.281269186 -0.462933899
## [378,] 0.145308323 -0.337470348 1.183817291 1.285154406 0.271835930
## [379,] -0.100434292 -0.148112235 0.886936726 0.259148546 0.704812541
## PC6
## [1,] 0.116709537
## [2,] 0.110173000
## [3,] 0.151011377
## [4,] -0.343807479
## [5,] -0.068417317
## [6,] -0.420280958
## [7,] 0.014839886
## [8,] 0.336718257
## [9,] -0.045952454
## [10,] 1.939826284
## [11,] -0.146897222
## [12,] 0.183314250
## [13,] 0.114162471
## [14,] -0.102727402
## [15,] 0.196911289
## [16,] -0.296960713
## [17,] -0.346683316
## [18,] 0.385229903
## [19,] 0.250212417
## [20,] 0.210997273
## [21,] 0.178758339
## [22,] -0.003801151
## [23,] 0.217319459
## [24,] -0.187966712
## [25,] -0.249408299
## [26,] 0.582504343
## [27,] -0.264956027
## [28,] -0.324073726
## [29,] 0.392690074
## [30,] 0.433561922
## [31,] -0.044052794
## [32,] -0.172924722
## [33,] -0.273046392
## [34,] -0.339264995
## [35,] 0.377235819
## [36,] -0.090271827
## [37,] 0.414287669
## [38,] -0.393701821
## [39,] 0.033505637
## [40,] 0.354862667
## [41,] 0.077217544
## [42,] -0.251343699
## [43,] 0.437209594
## [44,] 0.418033744
## [45,] 0.092143326
## [46,] 0.453442755
## [47,] 0.025217332
## [48,] -0.198309910
## [49,] 0.187074835
## [50,] 0.063584865
## [51,] 0.411945392
## [52,] 0.347020693
## [53,] -1.602200768
## [54,] -0.297652746
## [55,] 0.140534670
## [56,] -0.120117267
## [57,] 0.295188323
## [58,] -0.436240290
## [59,] -0.241532009
## [60,] -0.152644965
## [61,] -0.340782009
## [62,] -0.237639469
## [63,] 0.300926071
## [64,] -0.253457399
## [65,] -0.123036265
## [66,] -0.318934216
## [67,] 0.157579795
## [68,] -0.260813996
## [69,] -0.245354609
## [70,] -0.305254302
## [71,] -1.882250425
## [72,] 0.409598000
## [73,] 0.232202465
## [74,] -0.149057573
## [75,] 0.545903188
## [76,] 0.277588617
## [77,] 0.361912198
## [78,] -0.478016137
## [79,] -0.412381253
## [80,] -0.183130748
## [81,] 0.233456245
## [82,] -0.356154388
## [83,] 0.449569521
## [84,] -0.185788498
## [85,] -0.219609958
## [86,] -0.001711114
## [87,] -1.559617792
## [88,] -0.428893296
## [89,] -0.349853393
## [90,] 0.067731920
## [91,] 0.142796842
## [92,] -0.180830638
## [93,] 0.315292384
## [94,] 0.557663845
## [95,] -0.172373827
## [96,] 0.407727459
## [97,] 0.327538602
## [98,] 0.346056104
## [99,] 2.163269668
## [100,] 0.345529449
## [101,] 0.138719045
## [102,] -0.279523523
## [103,] -0.084975054
## [104,] 0.337408982
## [105,] 0.436700603
## [106,] 0.388716289
## [107,] 0.023800405
## [108,] -0.344894615
## [109,] 0.380430817
## [110,] 0.059212100
## [111,] -0.160062648
## [112,] 0.451808896
## [113,] -0.328134576
## [114,] -0.232509061
## [115,] 0.417691744
## [116,] -0.283499777
## [117,] -0.334241319
## [118,] -0.354492127
## [119,] 0.016626218
## [120,] 0.329368287
## [121,] 0.014802916
## [122,] 1.788209994
## [123,] -0.225290106
## [124,] -0.049381001
## [125,] -0.176037238
## [126,] -0.147416810
## [127,] 0.274931744
## [128,] -0.288402296
## [129,] -0.238830171
## [130,] -0.321394130
## [131,] -0.060804904
## [132,] -0.198430755
## [133,] -0.201882037
## [134,] -0.416230299
## [135,] -0.104823016
## [136,] -0.259292999
## [137,] 0.309515655
## [138,] 0.473433423
## [139,] -0.224455247
## [140,] -0.113549634
## [141,] -0.029270791
## [142,] -0.408139727
## [143,] -0.249679273
## [144,] 0.052432954
## [145,] 0.123609326
## [146,] 0.110721474
## [147,] 0.039482206
## [148,] -0.055563924
## [149,] -0.301541438
## [150,] 0.339761189
## [151,] -0.143565175
## [152,] 0.495882321
## [153,] -0.338275303
## [154,] -0.259013852
## [155,] -0.268105530
## [156,] -0.980893416
## [157,] -0.246803124
## [158,] -0.078306763
## [159,] 0.382030122
## [160,] 0.087323777
## [161,] 0.376505108
## [162,] 0.053401289
## [163,] -0.338300621
## [164,] -0.183747770
## [165,] 0.432642111
## [166,] 0.187719391
## [167,] -0.323645603
## [168,] 0.829006715
## [169,] 0.043491740
## [170,] -0.248046133
## [171,] -0.060255793
## [172,] -0.083545793
## [173,] -0.167508321
## [174,] -0.089468938
## [175,] -0.143831223
## [176,] 0.323860642
## [177,] -0.174432941
## [178,] -0.239734115
## [179,] 0.497289814
## [180,] -0.327540210
## [181,] -0.151688764
## [182,] 0.197182238
## [183,] -0.042715485
## [184,] 0.044010655
## [185,] -0.925270972
## [186,] 0.322942444
## [187,] -0.036587651
## [188,] 0.356359819
## [189,] 0.423139332
## [190,] -0.257850948
## [191,] 0.463686146
## [192,] -0.032295644
## [193,] -0.221120598
## [194,] 0.347410914
## [195,] -0.102882758
## [196,] -0.052886406
## [197,] 0.099771649
## [198,] 0.161046943
## [199,] 0.245795874
## [200,] 0.272924190
## [201,] 0.339839246
## [202,] 0.395294558
## [203,] -0.065386536
## [204,] 0.561844444
## [205,] -0.271407182
## [206,] -0.059059407
## [207,] 0.083045883
## [208,] 0.377344777
## [209,] 0.334594979
## [210,] 2.210117773
## [211,] -0.225352991
## [212,] 0.659498155
## [213,] 0.005821771
## [214,] -0.246898562
## [215,] 0.168733702
## [216,] -0.366893261
## [217,] -0.293117425
## [218,] 0.423293245
## [219,] -0.277523269
## [220,] 0.108760866
## [221,] 0.070710680
## [222,] 0.163384108
## [223,] -0.232906221
## [224,] 0.408184032
## [225,] -0.300209061
## [226,] -0.343281023
## [227,] 0.380266460
## [228,] 0.475769439
## [229,] -0.240418547
## [230,] 0.118544474
## [231,] 0.411577815
## [232,] -0.017746096
## [233,] -0.022662183
## [234,] -0.215224961
## [235,] -0.336453644
## [236,] -0.208327609
## [237,] 0.415886191
## [238,] 0.260849310
## [239,] -0.336942900
## [240,] -0.122484819
## [241,] -0.025660118
## [242,] 0.330693931
## [243,] 0.187450418
## [244,] 0.092254142
## [245,] -0.103389100
## [246,] -0.135338511
## [247,] -0.081072198
## [248,] 0.345962874
## [249,] -0.250967381
## [250,] -0.344899324
## [251,] -0.429960219
## [252,] -0.282830186
## [253,] 0.174435063
## [254,] -0.002994835
## [255,] -1.217412358
## [256,] 0.360421127
## [257,] -0.146287428
## [258,] -0.133025274
## [259,] -0.126146676
## [260,] 0.220778323
## [261,] 0.108029807
## [262,] 0.349752615
## [263,] 0.200005121
## [264,] -0.101933578
## [265,] -0.161334026
## [266,] 0.285586865
## [267,] -0.238563544
## [268,] 0.083679922
## [269,] 0.509906873
## [270,] -0.146139621
## [271,] 0.334416111
## [272,] 0.473647831
## [273,] 0.136442835
## [274,] -0.251405937
## [275,] 0.114366181
## [276,] 0.048022334
## [277,] -1.054946234
## [278,] -0.700681151
## [279,] -0.434292485
## [280,] 0.255500421
## [281,] -0.124820953
## [282,] -0.258508925
## [283,] 0.519297048
## [284,] 0.418680932
## [285,] -0.218443452
## [286,] -0.216123751
## [287,] 0.115923969
## [288,] -0.027866918
## [289,] -0.058716464
## [290,] -2.000384525
## [291,] 0.277974900
## [292,] -0.293421787
## [293,] -0.259635342
## [294,] 0.059625913
## [295,] 0.971487465
## [296,] -0.150615259
## [297,] -0.400937784
## [298,] 0.238954410
## [299,] -0.144937084
## [300,] 0.201952185
## [301,] -0.447834040
## [302,] 0.281901496
## [303,] -0.203869133
## [304,] -0.134202490
## [305,] -0.059036104
## [306,] -1.689975498
## [307,] 0.458648969
## [308,] 0.521154125
## [309,] 0.178933466
## [310,] 0.097184547
## [311,] 0.178727506
## [312,] -0.114849810
## [313,] -0.177928676
## [314,] 0.278091472
## [315,] -0.424718686
## [316,] 0.421376781
## [317,] -0.381796482
## [318,] -0.221941061
## [319,] -0.754255469
## [320,] 0.249838558
## [321,] -0.111526776
## [322,] -0.207650126
## [323,] -0.362767449
## [324,] 0.207891984
## [325,] 0.340268457
## [326,] 0.368766457
## [327,] 0.012058601
## [328,] -0.149559490
## [329,] 1.463155184
## [330,] 0.382942476
## [331,] -0.032112095
## [332,] 0.397084457
## [333,] -0.354911460
## [334,] -0.233823936
## [335,] 0.146812456
## [336,] -0.250028422
## [337,] 0.205107833
## [338,] -0.667916271
## [339,] -0.159417162
## [340,] 0.044940196
## [341,] 0.444365443
## [342,] 0.218371896
## [343,] -0.083864131
## [344,] -0.066718642
## [345,] 0.460637350
## [346,] 0.010040209
## [347,] -0.249703684
## [348,] 0.069849151
## [349,] 0.133553509
## [350,] -0.337335972
## [351,] 0.358285729
## [352,] 0.221064477
## [353,] -0.125296735
## [354,] -0.070458295
## [355,] -0.224997131
## [356,] 0.501370980
## [357,] -0.349367892
## [358,] 0.380452253
## [359,] -0.271394600
## [360,] -0.258419685
## [361,] 0.402658885
## [362,] -0.468027915
## [363,] -0.324990632
## [364,] 0.142034987
## [365,] -0.347928412
## [366,] -0.351391164
## [367,] -0.285977778
## [368,] -0.971457197
## [369,] -0.181523245
## [370,] -0.240725882
## [371,] 0.387573331
## [372,] -0.229079837
## [373,] -0.209054420
## [374,] 0.036780440
## [375,] 0.503922523
## [376,] -0.173505314
## [377,] -0.787406645
## [378,] 0.319960047
## [379,] 0.154968029
plot(Cancer_pca)
#get the original value of the data based on PCA
center <- Cancer_pca$center
scale <- Cancer_pca$scale
new_Cancer <- as.matrix(Cancer[,-1])
new_Cancer
## Age Stage Tumor Size Regional Node Examined Reginol Node Positive
## [1,] 68 1 4 24 1
## [2,] 50 2 35 14 5
## [3,] 58 3 63 14 7
## [4,] 58 1 18 2 1
## [5,] 47 2 41 3 1
## [6,] 51 1 20 18 2
## [7,] 51 1 8 11 1
## [8,] 40 2 30 9 1
## [9,] 40 4 103 20 18
## [10,] 69 4 32 21 12
## [11,] 68 1 13 9 1
## [12,] 46 3 59 11 3
## [13,] 65 2 35 13 3
## [14,] 48 1 15 23 7
## [15,] 62 2 35 16 14
## [16,] 61 1 19 20 1
## [17,] 56 2 46 1 1
## [18,] 43 2 24 22 1
## [19,] 48 2 25 16 1
## [20,] 60 2 29 20 1
## [21,] 48 2 30 15 2
## [22,] 57 2 40 15 5
## [23,] 55 2 29 4 1
## [24,] 48 3 70 18 1
## [25,] 62 1 20 26 22
## [26,] 63 2 22 31 17
## [27,] 48 2 50 25 23
## [28,] 46 1 17 14 1
## [29,] 57 2 25 14 4
## [30,] 66 2 21 10 1
## [31,] 47 2 40 3 1
## [32,] 53 1 15 5 1
## [33,] 59 1 15 6 1
## [34,] 60 1 20 19 3
## [35,] 46 2 30 19 10
## [36,] 51 1 10 9 2
## [37,] 54 2 27 21 6
## [38,] 51 1 18 14 2
## [39,] 49 2 35 10 2
## [40,] 51 2 23 15 5
## [41,] 57 3 70 12 12
## [42,] 64 1 17 12 2
## [43,] 62 2 21 2 1
## [44,] 53 2 23 15 6
## [45,] 55 1 5 11 2
## [46,] 66 3 51 10 5
## [47,] 42 1 9 15 2
## [48,] 62 1 15 12 1
## [49,] 53 2 32 16 9
## [50,] 69 1 5 8 3
## [51,] 37 2 23 17 3
## [52,] 69 3 55 9 1
## [53,] 60 3 120 7 1
## [54,] 63 3 77 20 2
## [55,] 57 1 2 16 1
## [56,] 55 1 11 13 1
## [57,] 62 2 25 19 1
## [58,] 50 1 18 49 1
## [59,] 50 1 15 15 1
## [60,] 55 1 12 17 2
## [61,] 56 1 18 24 2
## [62,] 51 1 17 12 1
## [63,] 42 2 26 1 1
## [64,] 59 3 75 20 2
## [65,] 67 1 13 16 3
## [66,] 46 1 15 5 1
## [67,] 31 3 70 23 23
## [68,] 40 1 15 20 3
## [69,] 58 1 15 5 1
## [70,] 52 1 17 12 3
## [71,] 49 3 130 12 8
## [72,] 64 2 34 24 20
## [73,] 31 2 30 16 1
## [74,] 66 1 10 15 1
## [75,] 67 2 22 19 16
## [76,] 56 3 55 13 1
## [77,] 66 2 25 11 4
## [78,] 42 2 50 7 1
## [79,] 51 2 50 9 1
## [80,] 68 1 15 9 1
## [81,] 53 2 30 21 13
## [82,] 67 1 20 10 1
## [83,] 66 2 22 9 2
## [84,] 53 1 15 2 1
## [85,] 51 1 15 13 1
## [86,] 46 2 40 12 11
## [87,] 48 3 120 7 5
## [88,] 52 3 80 10 1
## [89,] 55 1 17 11 1
## [90,] 65 1 3 9 1
## [91,] 53 3 60 8 1
## [92,] 33 1 14 15 1
## [93,] 63 2 26 5 4
## [94,] 45 2 25 21 16
## [95,] 59 1 12 12 3
## [96,] 60 2 25 17 2
## [97,] 50 2 30 4 2
## [98,] 61 2 25 10 1
## [99,] 50 4 24 3 3
## [100,] 68 2 27 14 1
## [101,] 38 3 70 33 24
## [102,] 47 1 16 25 1
## [103,] 39 2 45 3 1
## [104,] 57 2 27 7 1
## [105,] 52 2 23 14 3
## [106,] 60 2 25 2 1
## [107,] 54 2 40 11 1
## [108,] 68 1 20 12 2
## [109,] 38 2 21 8 2
## [110,] 63 2 36 30 3
## [111,] 61 1 14 15 4
## [112,] 37 3 51 3 3
## [113,] 46 2 50 34 10
## [114,] 45 2 45 14 2
## [115,] 54 3 51 6 5
## [116,] 53 1 19 12 3
## [117,] 50 3 76 9 1
## [118,] 69 1 20 16 9
## [119,] 48 2 35 15 3
## [120,] 53 2 27 15 2
## [121,] 67 2 35 7 2
## [122,] 43 4 35 15 3
## [123,] 50 2 50 16 16
## [124,] 59 2 38 23 4
## [125,] 53 1 15 23 2
## [126,] 62 1 17 16 1
## [127,] 39 2 25 13 2
## [128,] 59 1 19 3 1
## [129,] 56 1 15 8 2
## [130,] 45 1 18 13 3
## [131,] 60 1 11 14 1
## [132,] 50 2 45 10 6
## [133,] 58 1 12 8 1
## [134,] 50 1 20 5 1
## [135,] 55 2 45 8 7
## [136,] 37 1 18 28 5
## [137,] 46 2 25 12 1
## [138,] 65 2 21 20 1
## [139,] 61 2 49 14 10
## [140,] 52 3 70 18 9
## [141,] 54 1 7 4 1
## [142,] 36 1 19 13 4
## [143,] 49 1 17 24 1
## [144,] 62 2 38 23 3
## [145,] 54 2 34 20 1
## [146,] 61 2 30 15 1
## [147,] 46 1 4 18 2
## [148,] 38 3 72 13 8
## [149,] 66 1 18 1 1
## [150,] 59 2 25 13 3
## [151,] 38 1 9 18 1
## [152,] 67 2 21 14 2
## [153,] 60 1 20 15 1
## [154,] 61 1 15 14 5
## [155,] 67 1 18 14 2
## [156,] 69 3 100 16 6
## [157,] 47 1 17 15 1
## [158,] 39 1 7 6 1
## [159,] 53 2 24 2 1
## [160,] 55 2 43 14 14
## [161,] 59 2 30 18 4
## [162,] 53 1 7 3 1
## [163,] 59 1 18 2 1
## [164,] 57 1 12 20 2
## [165,] 61 2 25 16 6
## [166,] 68 3 62 3 1
## [167,] 54 1 20 12 7
## [168,] 37 4 70 24 17
## [169,] 48 2 37 8 1
## [170,] 53 1 13 14 1
## [171,] 69 2 40 20 2
## [172,] 63 3 70 11 3
## [173,] 49 1 12 9 2
## [174,] 63 1 9 9 1
## [175,] 60 1 10 24 2
## [176,] 41 3 55 11 1
## [177,] 59 1 18 17 10
## [178,] 43 1 15 7 2
## [179,] 52 2 25 31 14
## [180,] 61 2 50 11 5
## [181,] 60 1 10 32 1
## [182,] 61 2 30 23 2
## [183,] 63 1 13 3 1
## [184,] 48 2 40 15 13
## [185,] 51 3 100 14 11
## [186,] 66 2 25 14 2
## [187,] 68 3 68 3 3
## [188,] 58 2 25 14 2
## [189,] 62 2 23 34 9
## [190,] 46 1 15 14 1
## [191,] 58 2 22 12 1
## [192,] 60 1 7 2 1
## [193,] 62 1 16 19 4
## [194,] 53 2 24 5 1
## [195,] 42 3 75 16 13
## [196,] 63 1 11 5 1
## [197,] 55 2 35 16 2
## [198,] 50 3 60 10 5
## [199,] 52 2 30 22 2
## [200,] 47 2 25 11 2
## [201,] 55 2 25 14 2
## [202,] 60 2 25 16 4
## [203,] 66 1 12 1 1
## [204,] 50 2 25 17 12
## [205,] 64 1 17 2 1
## [206,] 67 1 11 6 1
## [207,] 56 2 32 24 1
## [208,] 60 2 21 18 1
## [209,] 56 2 25 12 1
## [210,] 48 4 19 6 1
## [211,] 44 3 75 11 4
## [212,] 37 3 52 17 12
## [213,] 52 1 9 18 17
## [214,] 63 1 17 9 1
## [215,] 54 2 35 10 9
## [216,] 63 3 85 4 4
## [217,] 44 2 50 12 1
## [218,] 68 3 51 17 1
## [219,] 64 1 18 4 2
## [220,] 50 3 75 27 27
## [221,] 55 3 72 14 13
## [222,] 66 2 35 20 7
## [223,] 46 1 12 18 2
## [224,] 43 2 23 9 3
## [225,] 43 1 16 2 1
## [226,] 43 1 16 27 2
## [227,] 59 3 57 20 9
## [228,] 55 3 50 42 1
## [229,] 61 1 17 9 1
## [230,] 66 2 32 15 4
## [231,] 55 2 21 19 1
## [232,] 65 1 11 7 7
## [233,] 69 2 40 22 5
## [234,] 59 1 15 2 1
## [235,] 63 1 17 15 2
## [236,] 68 1 14 26 1
## [237,] 48 3 60 26 21
## [238,] 61 3 55 12 1
## [239,] 43 4 120 28 26
## [240,] 44 1 11 8 2
## [241,] 47 2 39 29 1
## [242,] 52 2 23 30 2
## [243,] 69 2 28 9 2
## [244,] 39 2 37 18 15
## [245,] 43 2 40 15 5
## [246,] 64 1 9 18 1
## [247,] 66 1 8 9 1
## [248,] 45 2 28 18 3
## [249,] 37 1 15 15 2
## [250,] 50 1 17 11 1
## [251,] 40 2 50 6 6
## [252,] 52 2 48 5 1
## [253,] 41 2 30 2 2
## [254,] 32 3 68 13 6
## [255,] 65 3 110 19 2
## [256,] 67 2 23 20 2
## [257,] 57 1 12 13 2
## [258,] 63 1 13 7 1
## [259,] 42 2 40 20 1
## [260,] 57 2 30 12 1
## [261,] 42 1 9 11 2
## [262,] 46 2 22 9 1
## [263,] 47 2 30 9 2
## [264,] 67 1 12 3 3
## [265,] 67 1 10 33 1
## [266,] 65 2 25 3 1
## [267,] 65 1 16 33 1
## [268,] 33 3 65 3 3
## [269,] 64 2 22 4 1
## [270,] 66 1 17 20 10
## [271,] 34 3 60 13 9
## [272,] 55 2 22 20 2
## [273,] 47 2 35 18 3
## [274,] 58 1 18 9 9
## [275,] 38 2 34 11 1
## [276,] 57 1 6 2 1
## [277,] 65 3 105 4 2
## [278,] 52 3 100 23 17
## [279,] 67 1 20 14 2
## [280,] 57 3 57 14 3
## [281,] 61 1 10 16 1
## [282,] 45 1 17 12 2
## [283,] 50 2 25 18 10
## [284,] 50 2 21 12 2
## [285,] 53 2 45 14 2
## [286,] 54 2 50 7 6
## [287,] 58 2 35 13 2
## [288,] 56 2 38 12 11
## [289,] 68 1 16 30 28
## [290,] 41 3 140 41 15
## [291,] 61 2 25 39 1
## [292,] 65 1 18 17 1
## [293,] 69 1 18 11 1
## [294,] 43 2 34 19 6
## [295,] 47 4 65 14 14
## [296,] 67 1 13 10 1
## [297,] 45 1 20 1 1
## [298,] 65 2 29 11 4
## [299,] 53 1 10 21 1
## [300,] 67 3 62 13 3
## [301,] 43 2 50 18 1
## [302,] 47 2 29 23 2
## [303,] 48 1 15 30 3
## [304,] 62 1 15 46 14
## [305,] 68 2 42 25 5
## [306,] 57 3 130 10 10
## [307,] 40 2 21 22 3
## [308,] 56 3 51 10 4
## [309,] 52 2 30 4 1
## [310,] 40 2 35 19 3
## [311,] 51 2 31 4 2
## [312,] 67 1 14 15 5
## [313,] 54 1 15 14 6
## [314,] 56 3 60 27 17
## [315,] 48 1 20 12 1
## [316,] 57 2 22 4 1
## [317,] 47 3 80 14 1
## [318,] 54 1 15 14 3
## [319,] 41 3 100 28 23
## [320,] 65 2 30 12 1
## [321,] 58 1 8 18 1
## [322,] 38 1 15 15 1
## [323,] 38 3 80 8 3
## [324,] 60 2 30 19 7
## [325,] 58 2 25 16 1
## [326,] 63 2 24 15 6
## [327,] 53 2 35 14 4
## [328,] 43 1 12 1 1
## [329,] 60 4 45 9 1
## [330,] 60 2 25 10 9
## [331,] 47 2 35 24 1
## [332,] 48 2 28 19 2
## [333,] 59 1 17 6 3
## [334,] 56 1 15 19 1
## [335,] 53 2 32 13 1
## [336,] 48 1 15 11 2
## [337,] 52 3 60 4 1
## [338,] 61 3 90 13 2
## [339,] 66 1 11 19 3
## [340,] 45 2 37 13 4
## [341,] 52 2 21 12 3
## [342,] 67 1 2 19 9
## [343,] 40 3 70 17 1
## [344,] 50 1 8 9 1
## [345,] 65 2 22 23 5
## [346,] 55 2 40 12 12
## [347,] 47 1 13 5 1
## [348,] 49 2 32 16 2
## [349,] 53 1 5 29 9
## [350,] 53 1 18 17 2
## [351,] 44 3 52 24 4
## [352,] 54 2 31 16 4
## [353,] 51 1 14 6 1
## [354,] 46 1 7 7 1
## [355,] 47 1 12 1 1
## [356,] 68 2 21 18 1
## [357,] 50 1 20 23 2
## [358,] 67 2 26 5 2
## [359,] 47 1 16 3 1
## [360,] 68 1 15 20 1
## [361,] 55 2 25 10 2
## [362,] 47 1 20 23 1
## [363,] 56 3 80 24 3
## [364,] 51 2 30 2 2
## [365,] 41 1 16 11 2
## [366,] 67 1 20 16 4
## [367,] 58 1 17 19 7
## [368,] 67 3 100 25 8
## [369,] 63 2 41 14 4
## [370,] 69 1 16 12 6
## [371,] 59 2 25 30 11
## [372,] 44 4 108 16 14
## [373,] 65 1 12 2 1
## [374,] 48 2 38 24 4
## [375,] 39 2 24 26 13
## [376,] 55 2 45 14 13
## [377,] 50 3 98 14 12
## [378,] 39 2 25 16 3
## [379,] 49 2 30 18 1
## Survival Months
## [1,] 60
## [2,] 62
## [3,] 75
## [4,] 84
## [5,] 50
## [6,] 89
## [7,] 54
## [8,] 14
## [9,] 70
## [10,] 92
## [11,] 64
## [12,] 92
## [13,] 56
## [14,] 38
## [15,] 64
## [16,] 49
## [17,] 105
## [18,] 62
## [19,] 107
## [20,] 77
## [21,] 81
## [22,] 50
## [23,] 78
## [24,] 102
## [25,] 98
## [26,] 70
## [27,] 102
## [28,] 82
## [29,] 64
## [30,] 86
## [31,] 52
## [32,] 49
## [33,] 90
## [34,] 62
## [35,] 31
## [36,] 77
## [37,] 37
## [38,] 103
## [39,] 82
## [40,] 105
## [41,] 42
## [42,] 61
## [43,] 86
## [44,] 84
## [45,] 63
## [46,] 90
## [47,] 39
## [48,] 59
## [49,] 82
## [50,] 82
## [51,] 71
## [52,] 71
## [53,] 86
## [54,] 70
## [55,] 74
## [56,] 73
## [57,] 91
## [58,] 106
## [59,] 73
## [60,] 77
## [61,] 80
## [62,] 49
## [63,] 78
## [64,] 75
## [65,] 60
## [66,] 106
## [67,] 44
## [68,] 85
## [69,] 79
## [70,] 84
## [71,] 104
## [72,] 12
## [73,] 52
## [74,] 98
## [75,] 85
## [76,] 95
## [77,] 79
## [78,] 106
## [79,] 81
## [80,] 55
## [81,] 101
## [82,] 65
## [83,] 72
## [84,] 55
## [85,] 65
## [86,] 71
## [87,] 82
## [88,] 84
## [89,] 95
## [90,] 95
## [91,] 91
## [92,] 57
## [93,] 87
## [94,] 40
## [95,] 91
## [96,] 50
## [97,] 25
## [98,] 73
## [99,] 63
## [100,] 50
## [101,] 54
## [102,] 73
## [103,] 8
## [104,] 53
## [105,] 65
## [106,] 58
## [107,] 24
## [108,] 64
## [109,] 106
## [110,] 61
## [111,] 66
## [112,] 79
## [113,] 74
## [114,] 69
## [115,] 103
## [116,] 52
## [117,] 93
## [118,] 94
## [119,] 91
## [120,] 57
## [121,] 94
## [122,] 79
## [123,] 62
## [124,] 86
## [125,] 49
## [126,] 14
## [127,] 100
## [128,] 50
## [129,] 79
## [130,] 77
## [131,] 50
## [132,] 73
## [133,] 96
## [134,] 87
## [135,] 41
## [136,] 54
## [137,] 84
## [138,] 67
## [139,] 53
## [140,] 104
## [141,] 86
## [142,] 102
## [143,] 50
## [144,] 42
## [145,] 52
## [146,] 107
## [147,] 92
## [148,] 52
## [149,] 69
## [150,] 82
## [151,] 101
## [152,] 64
## [153,] 55
## [154,] 98
## [155,] 56
## [156,] 91
## [157,] 51
## [158,] 102
## [159,] 71
## [160,] 13
## [161,] 11
## [162,] 53
## [163,] 82
## [164,] 89
## [165,] 56
## [166,] 54
## [167,] 72
## [168,] 102
## [169,] 51
## [170,] 100
## [171,] 62
## [172,] 73
## [173,] 84
## [174,] 87
## [175,] 96
## [176,] 74
## [177,] 47
## [178,] 77
## [179,] 55
## [180,] 64
## [181,] 93
## [182,] 74
## [183,] 23
## [184,] 60
## [185,] 85
## [186,] 86
## [187,] 81
## [188,] 71
## [189,] 90
## [190,] 79
## [191,] 60
## [192,] 89
## [193,] 66
## [194,] 84
## [195,] 55
## [196,] 50
## [197,] 55
## [198,] 98
## [199,] 53
## [200,] 103
## [201,] 77
## [202,] 63
## [203,] 45
## [204,] 25
## [205,] 68
## [206,] 53
## [207,] 91
## [208,] 105
## [209,] 76
## [210,] 94
## [211,] 71
## [212,] 15
## [213,] 106
## [214,] 56
## [215,] 56
## [216,] 16
## [217,] 31
## [218,] 85
## [219,] 62
## [220,] 23
## [221,] 24
## [222,] 50
## [223,] 107
## [224,] 76
## [225,] 87
## [226,] 101
## [227,] 60
## [228,] 66
## [229,] 53
## [230,] 93
## [231,] 90
## [232,] 59
## [233,] 58
## [234,] 68
## [235,] 94
## [236,] 72
## [237,] 53
## [238,] 103
## [239,] 16
## [240,] 77
## [241,] 49
## [242,] 99
## [243,] 107
## [244,] 81
## [245,] 87
## [246,] 103
## [247,] 96
## [248,] 40
## [249,] 78
## [250,] 92
## [251,] 106
## [252,] 54
## [253,] 85
## [254,] 69
## [255,] 51
## [256,] 93
## [257,] 76
## [258,] 58
## [259,] 79
## [260,] 63
## [261,] 7
## [262,] 104
## [263,] 74
## [264,] 67
## [265,] 98
## [266,] 100
## [267,] 58
## [268,] 61
## [269,] 45
## [270,] 48
## [271,] 40
## [272,] 57
## [273,] 42
## [274,] 76
## [275,] 55
## [276,] 68
## [277,] 49
## [278,] 16
## [279,] 99
## [280,] 88
## [281,] 87
## [282,] 60
## [283,] 34
## [284,] 92
## [285,] 65
## [286,] 23
## [287,] 50
## [288,] 107
## [289,] 92
## [290,] 51
## [291,] 92
## [292,] 61
## [293,] 50
## [294,] 95
## [295,] 97
## [296,] 65
## [297,] 81
## [298,] 81
## [299,] 92
## [300,] 53
## [301,] 91
## [302,] 49
## [303,] 61
## [304,] 74
## [305,] 48
## [306,] 37
## [307,] 75
## [308,] 57
## [309,] 81
## [310,] 56
## [311,] 73
## [312,] 53
## [313,] 68
## [314,] 94
## [315,] 88
## [316,] 79
## [317,] 63
## [318,] 74
## [319,] 57
## [320,] 53
## [321,] 104
## [322,] 57
## [323,] 63
## [324,] 90
## [325,] 73
## [326,] 94
## [327,] 98
## [328,] 74
## [329,] 89
## [330,] 89
## [331,] 100
## [332,] 16
## [333,] 107
## [334,] 70
## [335,] 68
## [336,] 81
## [337,] 67
## [338,] 67
## [339,] 97
## [340,] 60
## [341,] 86
## [342,] 75
## [343,] 59
## [344,] 87
## [345,] 75
## [346,] 72
## [347,] 102
## [348,] 101
## [349,] 68
## [350,] 80
## [351,] 104
## [352,] 61
## [353,] 41
## [354,] 100
## [355,] 105
## [356,] 57
## [357,] 59
## [358,] 54
## [359,] 76
## [360,] 82
## [361,] 53
## [362,] 102
## [363,] 47
## [364,] 100
## [365,] 107
## [366,] 73
## [367,] 91
## [368,] 92
## [369,] 107
## [370,] 85
## [371,] 89
## [372,] 71
## [373,] 102
## [374,] 49
## [375,] 59
## [376,] 90
## [377,] 57
## [378,] 85
## [379,] 86
drop(scale(new_Cancer,center=center, scale=scale)%*%Cancer_pca$rotation[,1])
## [1] -1.493744354 0.426322428 1.694207768 -1.767583528 0.043714825
## [6] -1.028534021 -1.338771984 0.406514411 4.993025728 1.937948477
## [11] -1.756901401 1.296312778 -0.090142691 -0.076244034 1.004107956
## [16] -1.005634503 -0.538374841 0.204445317 -0.419443766 -0.252782392
## [21] -0.036353656 0.504291512 -0.618672209 1.459334722 0.693501261
## [26] 1.342457422 2.475721782 -1.137184838 -0.082096727 -0.951459346
## [31] 0.004306142 -1.358590305 -1.790419403 -0.908445651 1.245709794
## [36] -1.439873416 0.636390371 -1.304428696 -0.097417933 -0.188925650
## [41] 2.535953943 -1.364589888 -1.095258604 0.018958421 -1.483766860
## [46] 0.803570710 -0.776759752 -1.440160549 0.550199236 -1.959716237
## [51] 0.283946083 0.584420507 2.164109035 1.673683848 -1.630123732
## [56] -1.450559221 -0.534036352 -0.354843129 -1.178588655 -1.248535425
## [61] -0.944827480 -1.056029210 -0.473763736 1.681009012 -1.312786276
## [66] -1.639877002 4.455166578 -0.707613499 -1.710632794 -1.171903123
## [71] 3.302612150 2.121655213 0.528823585 -1.868775707 0.683905846
## [76] 0.821006546 -0.499967072 0.056071716 0.099588612 -1.638985742
## [81] 0.865297254 -1.545124764 -0.757282603 -1.494668798 -1.198962297
## [86] 1.053228198 2.839883593 1.506058603 -1.539415867 -2.166532837
## [91] 0.893002750 -0.677904182 -0.646604416 1.683330979 -1.509921397
## [96] -0.135237286 0.027644129 -0.637273583 1.070049729 -0.455435814
## [101] 4.600390311 -0.787145836 0.655142324 -0.428540034 -0.110654721
## [106] -0.734249607 0.296584193 -1.410702952 -0.418905210 0.446752555
## [111] -1.134059417 1.181466882 1.830654533 0.454774207 0.864920996
## [116] -0.897625868 1.357865125 -0.915336154 0.094948933 -0.037442692
## [121] -0.703244230 1.727474232 1.839479021 0.275373090 -0.732974709
## [126] -0.921856464 -0.151799435 -1.471716143 -1.483838817 -0.899242135
## [131] -1.358439633 0.549771469 -1.825714544 -1.466418848 0.713759778
## [136] 0.095641779 -0.311491252 -0.482193479 1.024336162 2.074951928
## [141] -1.891283328 -0.768896963 -0.660225602 0.458314079 0.202499186
## [146] -0.635694229 -1.314850127 2.618727317 -1.867933212 -0.390204192
## [151] -1.169108179 -0.593384345 -1.153893444 -1.299586961 -1.312753509
## [156] 2.158951805 -0.888545794 -1.604599290 -0.695240701 1.698058938
## [161] 0.523091631 -1.639464234 -1.775434759 -1.300191877 0.127243391
## [166] 0.728909729 -0.691130861 4.057107584 0.065928057 -1.537449988
## [171] 0.005212931 1.307010016 -1.400091197 -1.914378275 -1.354059138
## [176] 1.278137221 -0.240072950 -1.192542565 1.517499402 0.419667049
## [181] -1.183491054 -0.049231716 -1.497163756 1.362728567 3.022520941
## [186] -0.646848816 0.841699831 -0.341629561 0.597265999 -1.161264597
## [191] -0.477014120 -2.115125949 -0.991130507 -0.707735717 3.115036491
## [196] -1.696392904 0.151090645 1.330786502 0.296675856 -0.422623151
## [201] -0.318075869 -0.085308348 -1.822877611 1.201683038 -1.807181645
## [206] -1.784093888 -0.078106596 -0.721328123 -0.483839459 0.663630444
## [211] 1.978468906 2.937647970 -0.086636710 -1.481813930 0.623006822
## [216] 1.991882118 0.744165906 0.641119818 -1.586401627 4.773395918
## [221] 2.921320323 0.503935335 -1.241990069 -0.133856941 -1.486223026
## [226] -0.762041381 2.005021660 1.814305601 -1.411373860 -0.324175998
## [231] -0.456860329 -1.210396528 0.367888943 -1.737267642 -1.509987525
## [236] -1.290446225 3.655612544 0.611276361 6.711875034 -1.281390399
## [241] 0.776720455 0.008347450 -0.958826089 1.609087788 0.543831815
## [246] -1.795501728 -2.078996209 0.486998129 -0.821657492 -1.398504155
## [251] 0.526594325 0.120809384 -0.289560811 2.350354264 2.529945185
## [256] -0.594294620 -1.406577585 -1.651971076 0.415871178 -0.286827613
## [261] -0.645411407 -0.628353063 -0.136446586 -1.777655604 -1.357302997
## [266] -1.150407815 -0.854919366 1.748954057 -0.738423976 -0.346935263
## [271] 2.611945346 -0.054669716 0.590763284 -0.771766282 0.287407340
## [276] -1.904210848 1.980934953 4.349982486 -1.601460087 1.110817200
## [281] -1.635586546 -0.910449829 0.979721615 -0.472435837 0.298128461
## [286] 0.876478490 0.030556752 0.489276289 1.167193218 5.639123713
## [291] 0.076038156 -1.306362503 -1.492629535 0.548191410 3.173294742
## [296] -1.711510331 -1.420928885 -0.397038374 -1.338159554 1.238726422
## [301] 0.476798036 0.451358041 -0.410664267 0.631511135 0.606275351
## [306] 3.760469200 0.283257978 1.205872572 -0.547890175 0.675442079
## [311] -0.347420655 -1.082694803 -0.809911038 2.814192996 -1.219216145
## [316] -0.839858529 1.906604890 -1.128786006 4.980287452 -0.396555408
## [321] -1.686147468 -0.771587552 2.121003409 0.183525269 -0.388480855
## [326] -0.270374270 -0.016309255 -1.509365115 1.128006246 -0.013678857
## [331] 0.134239505 0.543266130 -1.694510184 -1.177192240 -0.154704801
## [336] -1.222393212 0.985284375 1.845084419 -1.537001279 0.486580696
## [341] -0.381846642 -1.058469609 1.953784231 -1.632770525 -0.069211481
## [346] 0.924645953 -1.679627649 -0.138978457 -0.306354427 -1.082397105
## [351] 1.560087096 0.213890453 -1.243101129 -1.723673624 -1.845736715
## [356] -0.533908899 -0.621852817 -0.663822556 -1.464448793 -1.523194528
## [361] -0.249284791 -0.978278825 2.298810986 -0.641761160 -1.237501132
## [366] -1.157403928 -0.796933393 2.646899548 -0.178975454 -1.330874437
## [371] 0.785519987 4.528600634 -2.215387412 0.852816653 1.528575274
## [376] 1.052831636 3.308075529 0.145308323 -0.100434292
predict(Cancer_pca)[,1]
## [1] -1.493744354 0.426322428 1.694207768 -1.767583528 0.043714825
## [6] -1.028534021 -1.338771984 0.406514411 4.993025728 1.937948477
## [11] -1.756901401 1.296312778 -0.090142691 -0.076244034 1.004107956
## [16] -1.005634503 -0.538374841 0.204445317 -0.419443766 -0.252782392
## [21] -0.036353656 0.504291512 -0.618672209 1.459334722 0.693501261
## [26] 1.342457422 2.475721782 -1.137184838 -0.082096727 -0.951459346
## [31] 0.004306142 -1.358590305 -1.790419403 -0.908445651 1.245709794
## [36] -1.439873416 0.636390371 -1.304428696 -0.097417933 -0.188925650
## [41] 2.535953943 -1.364589888 -1.095258604 0.018958421 -1.483766860
## [46] 0.803570710 -0.776759752 -1.440160549 0.550199236 -1.959716237
## [51] 0.283946083 0.584420507 2.164109035 1.673683848 -1.630123732
## [56] -1.450559221 -0.534036352 -0.354843129 -1.178588655 -1.248535425
## [61] -0.944827480 -1.056029210 -0.473763736 1.681009012 -1.312786276
## [66] -1.639877002 4.455166578 -0.707613499 -1.710632794 -1.171903123
## [71] 3.302612150 2.121655213 0.528823585 -1.868775707 0.683905846
## [76] 0.821006546 -0.499967072 0.056071716 0.099588612 -1.638985742
## [81] 0.865297254 -1.545124764 -0.757282603 -1.494668798 -1.198962297
## [86] 1.053228198 2.839883593 1.506058603 -1.539415867 -2.166532837
## [91] 0.893002750 -0.677904182 -0.646604416 1.683330979 -1.509921397
## [96] -0.135237286 0.027644129 -0.637273583 1.070049729 -0.455435814
## [101] 4.600390311 -0.787145836 0.655142324 -0.428540034 -0.110654721
## [106] -0.734249607 0.296584193 -1.410702952 -0.418905210 0.446752555
## [111] -1.134059417 1.181466882 1.830654533 0.454774207 0.864920996
## [116] -0.897625868 1.357865125 -0.915336154 0.094948933 -0.037442692
## [121] -0.703244230 1.727474232 1.839479021 0.275373090 -0.732974709
## [126] -0.921856464 -0.151799435 -1.471716143 -1.483838817 -0.899242135
## [131] -1.358439633 0.549771469 -1.825714544 -1.466418848 0.713759778
## [136] 0.095641779 -0.311491252 -0.482193479 1.024336162 2.074951928
## [141] -1.891283328 -0.768896963 -0.660225602 0.458314079 0.202499186
## [146] -0.635694229 -1.314850127 2.618727317 -1.867933212 -0.390204192
## [151] -1.169108179 -0.593384345 -1.153893444 -1.299586961 -1.312753509
## [156] 2.158951805 -0.888545794 -1.604599290 -0.695240701 1.698058938
## [161] 0.523091631 -1.639464234 -1.775434759 -1.300191877 0.127243391
## [166] 0.728909729 -0.691130861 4.057107584 0.065928057 -1.537449988
## [171] 0.005212931 1.307010016 -1.400091197 -1.914378275 -1.354059138
## [176] 1.278137221 -0.240072950 -1.192542565 1.517499402 0.419667049
## [181] -1.183491054 -0.049231716 -1.497163756 1.362728567 3.022520941
## [186] -0.646848816 0.841699831 -0.341629561 0.597265999 -1.161264597
## [191] -0.477014120 -2.115125949 -0.991130507 -0.707735717 3.115036491
## [196] -1.696392904 0.151090645 1.330786502 0.296675856 -0.422623151
## [201] -0.318075869 -0.085308348 -1.822877611 1.201683038 -1.807181645
## [206] -1.784093888 -0.078106596 -0.721328123 -0.483839459 0.663630444
## [211] 1.978468906 2.937647970 -0.086636710 -1.481813930 0.623006822
## [216] 1.991882118 0.744165906 0.641119818 -1.586401627 4.773395918
## [221] 2.921320323 0.503935335 -1.241990069 -0.133856941 -1.486223026
## [226] -0.762041381 2.005021660 1.814305601 -1.411373860 -0.324175998
## [231] -0.456860329 -1.210396528 0.367888943 -1.737267642 -1.509987525
## [236] -1.290446225 3.655612544 0.611276361 6.711875034 -1.281390399
## [241] 0.776720455 0.008347450 -0.958826089 1.609087788 0.543831815
## [246] -1.795501728 -2.078996209 0.486998129 -0.821657492 -1.398504155
## [251] 0.526594325 0.120809384 -0.289560811 2.350354264 2.529945185
## [256] -0.594294620 -1.406577585 -1.651971076 0.415871178 -0.286827613
## [261] -0.645411407 -0.628353063 -0.136446586 -1.777655604 -1.357302997
## [266] -1.150407815 -0.854919366 1.748954057 -0.738423976 -0.346935263
## [271] 2.611945346 -0.054669716 0.590763284 -0.771766282 0.287407340
## [276] -1.904210848 1.980934953 4.349982486 -1.601460087 1.110817200
## [281] -1.635586546 -0.910449829 0.979721615 -0.472435837 0.298128461
## [286] 0.876478490 0.030556752 0.489276289 1.167193218 5.639123713
## [291] 0.076038156 -1.306362503 -1.492629535 0.548191410 3.173294742
## [296] -1.711510331 -1.420928885 -0.397038374 -1.338159554 1.238726422
## [301] 0.476798036 0.451358041 -0.410664267 0.631511135 0.606275351
## [306] 3.760469200 0.283257978 1.205872572 -0.547890175 0.675442079
## [311] -0.347420655 -1.082694803 -0.809911038 2.814192996 -1.219216145
## [316] -0.839858529 1.906604890 -1.128786006 4.980287452 -0.396555408
## [321] -1.686147468 -0.771587552 2.121003409 0.183525269 -0.388480855
## [326] -0.270374270 -0.016309255 -1.509365115 1.128006246 -0.013678857
## [331] 0.134239505 0.543266130 -1.694510184 -1.177192240 -0.154704801
## [336] -1.222393212 0.985284375 1.845084419 -1.537001279 0.486580696
## [341] -0.381846642 -1.058469609 1.953784231 -1.632770525 -0.069211481
## [346] 0.924645953 -1.679627649 -0.138978457 -0.306354427 -1.082397105
## [351] 1.560087096 0.213890453 -1.243101129 -1.723673624 -1.845736715
## [356] -0.533908899 -0.621852817 -0.663822556 -1.464448793 -1.523194528
## [361] -0.249284791 -0.978278825 2.298810986 -0.641761160 -1.237501132
## [366] -1.157403928 -0.796933393 2.646899548 -0.178975454 -1.330874437
## [371] 0.785519987 4.528600634 -2.215387412 0.852816653 1.528575274
## [376] 1.052831636 3.308075529 0.145308323 -0.100434292
#The aboved two gives us the same thing. predict is a good function to know.
Cancer$Survivor <- as.factor(Cancer$Survivor)
out <- sapply(1:5, function(i){plot(Cancer$Survivor,Cancer_pca$x[,i],xlab=paste("PC",i,sep=""),ylab="Survivor")})
pairs(Cancer_pca$x[,1:5], ylim = c(-6,4),xlim = c(-6,4),panel=function(x,y,...){text(x,y,Cancer$Survivor)})
# Better Ways to Visualize
library(factoextra)
## Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
library(FactoMineR)
library(ggfortify)
library(psych)
##
## Attaching package: 'psych'
##
## The following object is masked from 'package:car':
##
## logit
##
## The following objects are masked from 'package:ggplot2':
##
## %+%, alpha
library(corrplot)
## corrplot 0.92 loaded
library(devtools)
## Loading required package: usethis
# Correlation
pairs.panels(Cancer[,-1],
gap = 0,
bg = c("red", "blue")[Cancer$Survivor],
pch=21)
fviz_eig(Cancer_pca, addlabels = TRUE)
fviz_pca_var(Cancer_pca,col.var = "cos2",
gradient.cols = c("#FFCC00", "#CC9933", "#660033", "#330033"),
repel = TRUE)
fviz_pca_ind(Cancer_pca, col.ind = "cos2",
gradient.cols = c("#FFCC00", "#CC9933", "#660033", "#330033"),
repel = TRUE)
biplot(Cancer_pca)
autoplot(Cancer_pca,
data = Cancer[,-1],
loadings = TRUE,
labels = Cancer$Survivor)
# Different PCA Method.
res.pca <- PCA(Cancer[,-1], graph = FALSE)
print(res.pca)
## **Results for the Principal Component Analysis (PCA)**
## The analysis was performed on 379 individuals, described by 6 variables
## *The results are available in the following objects:
##
## name description
## 1 "$eig" "eigenvalues"
## 2 "$var" "results for the variables"
## 3 "$var$coord" "coord. for the variables"
## 4 "$var$cor" "correlations variables - dimensions"
## 5 "$var$cos2" "cos2 for the variables"
## 6 "$var$contrib" "contributions of the variables"
## 7 "$ind" "results for the individuals"
## 8 "$ind$coord" "coord. for the individuals"
## 9 "$ind$cos2" "cos2 for the individuals"
## 10 "$ind$contrib" "contributions of the individuals"
## 11 "$call" "summary statistics"
## 12 "$call$centre" "mean of the variables"
## 13 "$call$ecart.type" "standard error of the variables"
## 14 "$call$row.w" "weights for the individuals"
## 15 "$call$col.w" "weights for the variables"
# Visualize and Interpret PCA using these functions
#get_eigenvalue(res.pca): Extract the eigenvalues/variances of principal components
#fviz_eig(res.pca): Visualize the eigenvalues
#get_pca_ind(res.pca), get_pca_var(res.pca): Extract the results for individuals and variables, respectively.
#fviz_pca_ind(res.pca), fviz_pca_var(res.pca): Visualize the results individuals and variables, respectively.
#fviz_pca_biplot(res.pca): Make a biplot of individuals and variables.
eig.val <- get_eigenvalue(res.pca)
eig.val
## eigenvalue variance.percent cumulative.variance.percent
## Dim.1 2.2378787 37.297979 37.29798
## Dim.2 1.1649997 19.416662 56.71464
## Dim.3 0.9784385 16.307309 73.02195
## Dim.4 0.9209868 15.349780 88.37173
## Dim.5 0.5100636 8.501061 96.87279
## Dim.6 0.1876326 3.127210 100.00000
fviz_eig(res.pca, addlabels = TRUE, ylim = c(0, 50))
var <- get_pca_var(res.pca)
#var$coord: coordinates of variables to create a scatter plot
#var$cos2: represents the quality of representation for variables on the factor map. It’s calculated as the squared coordinates: var.cos2 = var.coord * var.coord.
#var$contrib: contains the contributions (in percentage) of the variables to the principal components.
#The contribution of a variable (var) to a given principal component is (in percentage) : (var.cos2 * 100) / (total cos2 of the component).
var
## Principal Component Analysis Results for variables
## ===================================================
## Name Description
## 1 "$coord" "Coordinates for the variables"
## 2 "$cor" "Correlations between variables and dimensions"
## 3 "$cos2" "Cos2 for the variables"
## 4 "$contrib" "contributions of the variables"
# Coordinates
head(var$coord)
## Dim.1 Dim.2 Dim.3 Dim.4
## Age -0.3222059 0.2332281 -0.34538598 0.84965955
## Stage 0.8420261 -0.3528792 0.06110566 0.23471133
## Tumor Size 0.8709647 -0.3046266 -0.01417789 0.20513599
## Regional Node Examined 0.3553161 0.8128074 0.20888379 -0.02009270
## Reginol Node Positive 0.6867038 0.4740946 0.01662008 -0.01753655
## Survival Months -0.2620363 -0.0886666 0.90072386 0.31809437
## Dim.5
## Age 0.02389842
## Stage -0.13460531
## Tumor Size -0.09635083
## Regional Node Examined -0.41115983
## Reginol Node Positive 0.55012576
## Survival Months 0.10197883
# Cos2: quality on the factore map
head(var$cos2)
## Dim.1 Dim.2 Dim.3 Dim.4
## Age 0.10381664 0.054395332 0.1192914718 0.7219213433
## Stage 0.70900791 0.124523708 0.0037339019 0.0550894103
## Tumor Size 0.75857952 0.092797395 0.0002010125 0.0420807734
## Regional Node Examined 0.12624954 0.660655847 0.0436324379 0.0004037167
## Reginol Node Positive 0.47156209 0.224765673 0.0002762270 0.0003075306
## Survival Months 0.06866303 0.007861765 0.8113034757 0.1011840305
## Dim.5
## Age 0.0005711344
## Stage 0.0181185895
## Tumor Size 0.0092834832
## Regional Node Examined 0.1690524091
## Reginol Node Positive 0.3026383510
## Survival Months 0.0103996819
# Contributions to the principal components
head(var$contrib)
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5
## Age 4.639064 4.6691283 12.19202521 78.38563371 0.1119732
## Stage 31.682142 10.6887329 0.38161845 5.98156347 3.5522213
## Tumor Size 33.897258 7.9654435 0.02054421 4.56909623 1.8200637
## Regional Node Examined 5.641483 56.7086700 4.45939492 0.04383523 33.1433948
## Reginol Node Positive 21.071834 19.2931955 0.02823141 0.03339143 59.3334482
## Survival Months 3.068220 0.6748298 82.91818582 10.98647993 2.0388989
#The plot Below is also known as variable correlation plots. It shows the relationships between all variables. It can be interpreted as follow:
#Positively correlated variables are grouped together.
#Negatively correlated variables are positioned on opposite sides of the plot origin (opposed quadrants).
#The distance between variables and the origin measures the quality of the variables on the factor map.
#Variables that are away from the origin are well represented on the factor map.
# Correlation circle
fviz_pca_var(res.pca, col.var = "black")
# Quality of representation
corrplot(var$cos2, is.corr=FALSE)
# Total cos2 of variables on Dim.1 and Dim.2
#A high cos2 indicates a good representation of the variable on the principal component.
#In this case the variable is positioned close to the circumference of the correlation circle.
#A low cos2 indicates that the variable is not perfectly represented by the PCs.
#In this case the variable is close to the center of the circle.
fviz_cos2(res.pca, choice = "var", axes = 1:2)
fviz_pca_var(res.pca, col.var = "cos2",
gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
repel = TRUE # Avoid text overlapping
)
# Change the transparency by cos2 values
fviz_pca_var(res.pca, alpha.var = "cos2")
corrplot(var$contrib, is.corr=FALSE)
# Contributions of variables to PC1
fviz_contrib(res.pca, choice = "var", axes = 1, top = 10)
# Contributions of variables to PC2
# Description of PC
res.desc <- dimdesc(res.pca, axes = c(1,2,3,4,5), proba = 0.05)
# Description of dimension 1
res.desc$Dim.1
##
## Link between the variable and the continuous variables (R-square)
## =================================================================================
## correlation p.value
## Tumor Size 0.8709647 2.118538e-118
## Stage 0.8420261 4.258836e-103
## Reginol Node Positive 0.6867038 3.629109e-54
## Regional Node Examined 0.3553161 1.015769e-12
## Survival Months -0.2620363 2.277214e-07
## Age -0.3222059 1.326702e-10
res.desc$Dim.2
##
## Link between the variable and the continuous variables (R-square)
## =================================================================================
## correlation p.value
## Regional Node Examined 0.8128074 1.692844e-90
## Reginol Node Positive 0.4740946 1.235575e-22
## Age 0.2332281 4.455756e-06
## Tumor Size -0.3046266 1.400911e-09
## Stage -0.3528792 1.483228e-12
res.desc$Dim.3
##
## Link between the variable and the continuous variables (R-square)
## =================================================================================
## correlation p.value
## Survival Months 0.9007239 1.380762e-138
## Regional Node Examined 0.2088838 4.160170e-05
## Age -0.3453860 4.655452e-12
res.desc$Dim.4
##
## Link between the variable and the continuous variables (R-square)
## =================================================================================
## correlation p.value
## Age 0.8496595 8.117074e-107
## Survival Months 0.3180944 2.334655e-10
## Stage 0.2347113 3.857241e-06
## Tumor Size 0.2051360 5.740140e-05
res.desc$Dim.5
##
## Link between the variable and the continuous variables (R-square)
## =================================================================================
## correlation p.value
## Reginol Node Positive 0.5501258 2.302831e-31
## Survival Months 0.1019788 4.726330e-02
## Stage -0.1346053 8.695976e-03
## Regional Node Examined -0.4111598 6.817718e-17
# Graph of Indiviuals
ind <- get_pca_ind(res.pca)
ind
## Principal Component Analysis Results for individuals
## ===================================================
## Name Description
## 1 "$coord" "Coordinates for the individuals"
## 2 "$cos2" "Cos2 for the individuals"
## 3 "$contrib" "contributions of the individuals"
## Principal Component Analysis Results for individuals
## ===================================================
## Name Description
## 1 "$coord" "Coordinates for the individuals"
## 2 "$cos2" "Cos2 for the individuals"
## 3 "$contrib" "contributions of the individuals"
#To get access to the different components, use this:
# Coordinates of individuals
head(ind$coord)
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5
## 1 -1.49571890 1.6749148 -0.79882567 0.6402257 -0.85340433
## 2 0.42688597 -0.1242504 -0.22240645 -0.4786708 0.01494530
## 3 1.69644730 -0.5458449 0.07002965 1.0340669 0.03911005
## 4 -1.76992006 -0.8864728 -0.03088789 0.2089963 0.77293051
## 5 0.04377261 -1.6055077 -0.90431537 -0.8507928 0.07847539
## 6 -1.02989362 0.5034039 0.86504682 -0.4218416 -0.23355708
# Quality of individuals
head(ind$cos2)
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5
## 1 0.3274322470 0.41058866 0.093395406 0.059991224 0.1065936095
## 2 0.3729259505 0.03159324 0.101226350 0.468891786 0.0004570965
## 3 0.6732837945 0.06970372 0.001147311 0.250158183 0.0003578443
## 4 0.6695024705 0.16794832 0.000203902 0.009335167 0.1276808541
## 5 0.0004637016 0.62381877 0.197912619 0.175178687 0.0014903924
## 6 0.4290771448 0.10251416 0.302712164 0.071986248 0.0220666662
# Contributions of individuals
head(ind$contrib)
## Dim.1 Dim.2 Dim.3 Dim.4 Dim.5
## 1 0.2637692749 0.635360823 0.1720803475 0.11742853 0.3767437880
## 2 0.0214856261 0.003496474 0.0133389606 0.06564190 0.0001155435
## 3 0.3393165082 0.067479762 0.0013224861 0.30634069 0.0007912489
## 4 0.3693444212 0.177977767 0.0002572787 0.01251367 0.3090418632
## 5 0.0002259067 0.583794159 0.2205296909 0.20737433 0.0031856891
## 6 0.1250572789 0.057394224 0.2017931729 0.05098076 0.0282177573
fviz_pca_ind(res.pca)
fviz_pca_ind(res.pca, col.ind = "cos2",
gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
repel = TRUE # Avoid text overlapping (slow if many points)
)
fviz_pca_ind(res.pca, pointsize = "cos2",
pointshape = 21, fill = "#E7B800",
repel = TRUE # Avoid text overlapping (slow if many points)
)
fviz_pca_ind(res.pca, col.ind = "cos2", pointsize = "cos2",
gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
repel = TRUE # Avoid text overlapping (slow if many points)
)
fviz_cos2(res.pca, choice = "ind")
# Total contribution on PC1 and PC2
fviz_contrib(res.pca, choice = "ind", axes = 1:2)
# Create a random continuous variable of length 23,
# Same length as the number of active individuals in the PCA
set.seed(123)
my.cont.var <- rnorm(49)
# Color individuals by the continuous variable
fviz_pca_ind(res.pca,
geom.ind = "point", # show points only (nbut not "text")
col.ind = Cancer$Survivor, # color by groups
palette = c("#00AFBB", "#E7B800", "#FC4E07"),
addEllipses = TRUE, # Concentration ellipses
legend.title = "Groups"
)
fviz_pca_ind(res.pca, geom.ind = "point", col.ind = Cancer$Survivor,
palette = c("#00AFBB", "#E7B800", "#FC4E07"),
addEllipses = TRUE, ellipse.type = "confidence",
legend.title = "Groups"
)
fviz_pca_ind(res.pca,
label = "none", # hide individual labels
habillage = Cancer$Survivor, # color by groups
addEllipses = TRUE, # Concentration ellipses
palette = "jco"
)
fviz_pca_var(res.pca, geom.var = c("point", "text"))
# Show individuals text labels only
fviz_pca_ind(res.pca, geom.ind = "text")
# Change the size of arrows an labels
fviz_pca_var(res.pca, arrowsize = 1, labelsize = 5,
repel = TRUE)
# Change points size, shape and fill color
# Change labelsize
fviz_pca_ind(res.pca,
pointsize = 3, pointshape = 21, fill = "lightblue",
labelsize = 5, repel = TRUE)
fviz_pca_ind(res.pca,
geom.ind = "point", # show points only (but not "text")
group.ind = Cancer$Survivor, # color by groups
legend.title = "Groups",
mean.point = FALSE)
fviz_pca_ind(res.pca,
geom.ind = "point", # show points only (but not "text")
group.ind = Cancer$Survivor, # color by groups
legend.title = "Groups",
mean.point = TRUE)
fviz_pca_var(res.pca, axes.linetype = "blank")
ind.p <- fviz_pca_ind(res.pca, geom = "point", col.ind = Cancer$Survivor)
ggpubr::ggpar(ind.p,
title = "Principal Component Analysis",
subtitle = "Iris data set",
caption = "Source: factoextra",
xlab = "PC1", ylab = "PC2",
legend.title = "Survivor", legend.position = "top",
ggtheme = theme_gray(), palette = "jco"
)
fviz_pca_biplot(res.pca, repel = TRUE,col.ind = Cancer$Survivor,
col.var = "#2E9FDF", # Variables color
)
fviz_pca_biplot(res.pca,
col.ind = Cancer$Survivor, palette = "jco",
addEllipses = TRUE, label = "var",
col.var = "black", repel = TRUE,
legend.title = "Survivorship")
fviz_pca_biplot(res.pca,
# Fill individuals by groups
geom.ind = "point",
pointshape = 21,
pointsize = 2.5,
fill.ind = Cancer$Survivor,
col.ind = "black",
# Color variable by groups
legend.title = list(fill = "Survivor", color = "Clusters"),
repel = TRUE # Avoid label overplotting
)+
ggpubr::fill_palette("jco")+ # Indiviual fill color
ggpubr::color_palette("npg") # Variable colors
fviz_pca_biplot(res.pca,
# Individuals
geom.ind = "point",
fill.ind = Cancer$Survivor, col.ind = "black",
pointshape = 21, pointsize = 2,
palette = "jco",
addEllipses = TRUE,
# Variables
alpha.var ="contrib", col.var = "contrib",
gradient.cols = "RdYlBu",
legend.title = list(fill = "Survivor", color = "Contrib",
alpha = "Contrib")
)
# ANOVA
summary(aov(Cancer$Stage ~ Cancer$Survivor))
## Df Sum Sq Mean Sq F value Pr(>F)
## Cancer$Survivor 1 8.38 8.379 13.81 0.000233 ***
## Residuals 377 228.78 0.607
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
summary(aov(Cancer$Age ~ Cancer$Survivor))
## Df Sum Sq Mean Sq F value Pr(>F)
## Cancer$Survivor 1 5 4.91 0.058 0.809
## Residuals 377 31774 84.28
# MANOVA
summary(manova(as.matrix(Cancer[,-1])~ Cancer$Survivor))
## Df Pillai approx F num Df den Df Pr(>F)
## Cancer$Survivor 1 0.27145 23.1 6 372 < 2.2e-16 ***
## Residuals 377
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1